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Assessment Summary

ISRP Assessment 2002-002-00-ISRP-20120215
Assessment Number: 2002-002-00-ISRP-20120215
Project: 2002-002-00 - Kootenai River Habitat Restoration Program
Review: Resident Fish, Regional Coordination, and Data Management Category Review
Proposal Number: RESCAT-2002-002-00
Completed Date: 4/16/2012
Final Round ISRP Date: 4/3/2012
Final Round ISRP Rating: Meets Scientific Review Criteria (Qualified)
Final Round ISRP Comment:

Additional comment on the response and more detail on the qualifications described above are provided below.

I. More detail on the feasibility assessments and design activities for phase 2 and 3 projects should be presented.

A considerable amount of additional detail was provided about the process used to identify and prioritize Phase 2 and Phase 3 projects. The response relied heavily on the KRHRP Master Plan, referring to this document rather than providing information in the response. The ISRP review would have been greatly facilitated if the sponsors had summarized the pertinent parts of the plan and included them in the proposal. The response stresses the reliance on the adaptive management process and indicates that Phase 2 and Phase 3 projects will be modified based on monitoring results generated from the implementation of Phase 1 projects or the nutrient enhancement and reconnect projects. However, the time between Phase 1 and Phases 2 and 3may be too short to obtain any conclusive indication of project effectiveness. Scheduling future restoration efforts to take maximum advantage of the information being collected from existing projects should be considered.

II. A draft of the KRHRP monitoring and adaptive management plan should be provided. 

As noted above, a link to the draft plan was provided with the response. Although this document describes a generalized adaptive management approach for the project area, it fails to specify how adaptive management will be applied at the project level. Adaptive management processes for each project should be developed and linked to the framework articulated in the subbasin plan. The project level RM&E effort also should incorporate some level of biological monitoring (see qualification above). An understanding of the biological responses by the focal species to individual projects is necessary to determine the extent to which particular restoration efforts are contributing to changes in population attributes detected by the systemwide biological monitoring efforts on the Kootenai River.

 III. Ten recruitment failure hypotheses are listed in the proposal. Identify which of these hypotheses have been tested and what conclusions have been reached.

To date, the relative validity of the 10 recruitment-failure hypotheses has been investigated largely through the application of a structured expert-opinion process. This effort represents a good method of prioritizing experiments to verify the accuracy of these opinions. This should be a near-term RM&E priority.

IV. Summarize the history and results from spill tests resulting from the suit by the Center for Biological Diversity (CBD) in 2003 that concerned the RPA in the 2000 Biological Opinion and the designation of Kootenai sturgeon critical habitat.

A summary of the results, to date, of the various spill tests from Libby Dam were provided in the response. This information adequately addressed the ISRP concern.

 V. There are three other projects on the Kootenai River that are closely related to this proposal. Describe how this project connects with these projects.

As noted in the qualifications, the administrative relationships among the various projects were adequately described. However, the manner in which information generated by the various projects was being synthesized and interpreted was not explained in the response or in the subbasin adaptive management plan. The ISRP suggests that a multi-project synthesis of the research and monitoring results generated to date be completed.

Additional Minor Comments

This project is entitled “Restore Natural Recruitment of Kootenai River White Sturgeon” in Taurus but also was referred to as “Kootenai River Habitat Restoration Project.” Which is the correct name? Projects should be labeled consistently and should reveal the main thrust of the project.

The ISRP was also concerned that although the project indicated that an “ecosystem approach” was being employed for this project, it seems to be very focused only on the focal species. Other native species receive very little attention in the proposal. The response to the concern about this issue provided some information about studies being conducted on cottids, mostly related to potential predation impacts on focal species. It would be useful for the project sponsors to consider if there are some other native indicator species, such as other fishes or macroinvertebrate species, that could provide an indication of an ecosystem-level response that may not be reflected by monitoring the focal species alone.

The project sponsors did a thorough job of addressing some of the ISRP comments on the original proposal. However, there are several issues that still need to be considered prior to proceeding with this project: See qualifications.

Modified by Dal Marsters on 4/16/2012 10:44:20 PM.
Qualification #1 - Qualification #1 - biological assessment should be included at the project-level
The response indicates that project-scale monitoring will be limited to assessment of the effects of the project on habitat condition. In order to determine the manner in which a specific restoration project is affecting one of the focal species, some level of biological assessment should be included at the project-level. The quality of the biological monitoring at the whole-system level appears to be very complete on the Kootenai River and should provide a good indication of how populations of the focal species are changing over time. However, the ability to associate a change in demographics with restoration efforts will require some level of understanding of the focal species' response at the project sites.
Qualification #2 - Qualification #2 - Specific adaptive management components for each project should be developed
A link to a draft of the KRH-RP subbasin adaptive management plan was provided. This document is still under development, and additional detail will be added over time. The plan provides a generalized process for structured decision making about the Kootenai River projects but does not contain enough detail to understand how adaptive management will be achieved at a project scale. Specific adaptive management components for each project should be developed and linked to the subbasin adaptive management plan. The ISRP's programmatic comments on Structured Decision Management in this report provide some additional information on this point.
Qualification #3 - Qualification #3 - white sturgeon in Kootenay Lake and the possible interaction with the river population
The hypothesis raised by the ISRP concerning a larger and relatively unknown sub-population of white sturgeon in Kootenay Lake and the possible interaction with the river population should be considered more completely.
Qualification #4 - Qualification #4 - be more aggressive about publishing the results of the research
The response provides an explanation of the administrative relationships among the various Kootenai River projects. However, an explanation of how RM&E results generated by these various projects are being integrated and interpreted was not included in the response. Some of the projects have been have underway for a number of years and have collected a considerable amount of data. A synthesis of the results obtained across all these projects relative to addressing the two key objectives listed on page 14: (Restore and maintain Kootenai River habitat conditions that support all life stages of Endangered Species Act listed Kootenai River white sturgeon; Restore and maintain Kootenai River habitat conditions that support all life stages of native Kootenai subbasin focal fish species) would be a very useful exercise. The project results are presented in the KTOI proposals largely as lists of parameters being measured. To take full advantage of the wealth of information being generated, these data should be synthesized and interpreted. The synthesis should not be a simple tabulation of data collected but a concise and comprehensive interpretation of these data that can be used to guide current and future restoration efforts on this system. This qualification has been applied to all Kootenai River projects currently being reviewed (199404900, 200200800, and 200200200). A review of the ocean research being funded by BPA was recently completed and could serve as a template for a synthesis report on the Kootenai River. The sponsors of all the Kootenai River projects should also be more aggressive about publishing the results of the research being conducted on the river and floodplain. These are very large projects with the potential to be a model for river/floodplain restoration. However, the experiences gained through the implementation of these projects cannot be effectively shared unless this information is published.
Qualification #5 - Qualification #5 - focus on the experimental evaluation
The ISRP requested some additional information regarding the extent to which the 10 recruitment failure hypotheses had been experimentally tested. The response indicated that there has been relatively little experimental testing of these hypotheses. Their relative validity has been assessed by a very highly qualified expert panel using a subjective scoring system. Expert opinion has considerable value, especially if it is applied using an organized process as was done here. However, expert opinion falls quite short of accepting or rejecting a hypothesis based on specific field data. The RM&E effort in the near term should focus on the experimental evaluation of those hypotheses deemed to be most likely limiting sturgeon recruitment.
First Round ISRP Date: 2/8/2012
First Round ISRP Rating: Response Requested
First Round ISRP Comment:

Responses requested:

  1. More detail on the feasibility assessments and design activities for phase 2 and 3 projects should be presented.
  2. A draft of the KRHRP monitoring and adaptive management plan should be provided.
  3. Ten recruitment failure hypotheses are listed in the proposal. Identify which of these hypotheses have been tested and what conclusions have been reached.
  4. Summarize the history and results from spill tests resulting from the suit by the Center for Biological Diversity (CBD) in 2003 that concerned the RPA in the 2000 Biological Opinion and the designation of Kootenai sturgeon critical habitat.
  5. There are three other projects on the Kootenai River that are closely related to this proposal. Describe how this project connects with these projects.

This proposal describes a large project that is almost a program in itself. This is a worthwhile effort and has already made some progress towards meeting program objectives. However, some of the very ambitious projects included in this proposal are not described in sufficient detail to determine if they would make a significant contribution to meeting program objectives. The understanding of the factors limiting recruitment of white sturgeon is incomplete. However, the sponsors are relying extensively on the theory that the limiting factors for white sturgeon is at the eggs/larvae stage. It would be useful to provide evidence that focusing on improved survival of this life stage has contributed to recovery of other sturgeon populations around the world.

More detail on the feasibility assessments and design activities for phase 2 and 3 projects should be included. This project is very large and complicated. Essentially, the proposal is for a habitat restoration program in which projects are funded prior to the completion of planning and design. The fact that the program proposes to proceed without a clear identification of limiting factors or specific desired population objectives for the focal species suggests that a more conservative approach might be advisable. Support for projects already initiated and O&M for existing projects could be supported through this proposal with Phase 2 and 3 projects included in subsequent funding requests, once understanding of limiting factors is improved and a full project feasibility assessment and design has been completed.

The KRHRP monitoring and adaptive management plan appears to be viewed as the coordinating structure for the RME program at the subbasin scale. This plan is scheduled for completion in 2012. Review of the RME component of this proposal is not possible without the inclusion of this plan. The revised proposal should have the plan, or at least a draft, appended to the proposal.

There are three other projects on the Kootenai River that are closely related to this proposal. The connections among the four projects are never fully described in any of the four proposals.

1. Purpose: Significance to Regional Programs, Technical Background, and Objectives

This is a large project of major significance to a variety of agencies and stakeholders in a large reach of the Kootenai River. The project represents a substantial effort to restore aquatic habitat conditions in a large river that supports a number of ESA listed fish species. Most of the background information is provided in the Major Accomplishments section and is generally adequate. However, the sponsors claim that only the Kootenai River supports a naturally landlocked population of white sturgeon is incorrect. The Nechako River in BC has a non-anadromous population and several relevant papers on this stock were not cited (e.g., McAdam et al. 2005; McAdam et al. 2011). It might be instructive for the sponsors to review literature from the Nechako.

OBJ-1: “Restore and maintain Kootenai River habitat conditions that support all life stages of Endangered Species Act listed Kootenai River white sturgeon” and OBJ-2: “Restore and maintain Kootenai River habitat conditions that support all life stages of native Kootenai subbasin focal fish species” are really stated as general rather than quantitative objectives. The objectives should be specific and measurable. Linking the objectives with the deliverables partially addresses this concern. Nonetheless, it would be helpful if the objectives were more quantitative and included measures of incremental success. Given that the required habitat conditions needed to recover and support white sturgeon are not completely known, these objectives should include both habitat and demographic targets and be closely linked to the RME effort associated with this project so objectives can be amended as knowledge improves.

In addition, the objectives appear to concentrate heavily on the focal species to the exclusion of others. This approach is not ecosystem restoration. It would be helpful to discuss how the restoration actions proposed also will benefit burbot, salmonids and other species such as cottids, which are not ESA listed or harvested but are important for trophodynamics and predation (see below; McAdam 2011). A possible approach would be the application of trophic models to assess the extent to which the bioenergetics needs of focal species will be met by the various measures being taken to improve food supply (e.g., Bevelhimer 2002; van Poorten and McAdam 2010). This comment also applies to the Ball Creek and Floodplain reconnection projects.

2. History: Accomplishments, Results, and Adaptive Management (ISRP Review of Results)

This project has a relatively long history, and the proposal includes a very good review of the ecological and legal issues around Kootenai white sturgeon. The sponsors have provided a good description of the rather tortuous path they have followed in order to develop the Master Plan (1997-2010). The ISRP appreciated the on-line access to the extensive library of project documents although some (e.g., Kynard et al. 2010) could not be downloaded completely. The vast majority of the literature is grey, however.

Several habitat restoration projects have already been implemented on the Kootenai, but there was little evidence in the proposal that the response of the focal species to these projects has been assessed. The sponsors did state, “Since 2005 the Tribe, in response to Recovery Team guidance, has released either fertilized eggs or free-embryos into reaches of the Kootenai River that have more suitable rocky substrates. The releases have ranged from 400,000 to over one million fertilized eggs or free-embryos annually. To date these experimental releases have not produced a detected increase in captured unmarked juvenile Kootenai sturgeon (Rust 2010).” It would be helpful to put these findings in the context of the recent laboratory experiments reported by Kynard et al (2010) (cited in the document) and McAdam (2011). The propensity of larvae to drift, as well as predation by cottids, was clearly related to substrate size; when gravel and cobble was provided the larvae hid and had lower mortality. Although subject to the usual caveats of lab work, these results have important implications for sturgeon habitat restoration in the Kootenai River. First, the proposal to create spawning substrate in the meander and other reaches should carefully consider bed load movement of mud and sand and the possibility that desirable substrate will be rapidly covered. Second, ecosystem restoration by nutrient addition and other methods could result in increased cottid populations which could increase predation pressure.

In their response to the ISRP’s review of their (STEP) sturgeon and burbot hatchery proposal the sponsors state, “Biological responses to the collective measures associated with the Tribe’s different habitat restoration and nutrient projects is a key component of the program-wide adaptive management approach currently under development. The extent to which sturgeon may benefit from these actions is unknown, but it is likely that improved ecosystem function, habitat complexity, and productivity could be beneficial” (see ISRP 2010-27). Because sturgeon live a very long time, the monitoring work will have to go on at the decade scale in order to assess fish response.

The adaptive management process for the Kootenai River projects is to be described in a plan to be completed in 2012. Because this plan was not included with the proposal, it is difficult to judge the adequacy of the adaptive management process. In addition, the description of the organizational structure intended to implement adaptive management was unclear. According to the proposal there are five teams involved in adaptive management (PeerReviewer Advisory Team [PRAT]; Modeling Review Team; Core Adaptive Management Team [CAMT]: Co-manager and Agency Review Team [CMART]: Kootenai Habitat Policy Team). It would be helpful to include a description of how these groups interact and decide priorities as they relate to RME.

ISRP Retrospective Evaluation of Results

Information on the results of previous projects and studies was provided in the proposal and links to other documents providing this information was provided. However, additional focus should be placed on developing syntheses from information that has been collected to date. These syntheses would be valuable for the formulation of testable hypotheses/relationships that will guide the generation information useful for informing managers and guiding future RME efforts. More extensive application of predictive models also may help in this regard.

3. Project Relationships, Emerging Limiting Factors, and Tailored Questions for Type of Work (hatchery, RME, tagging)

There are three other projects on the Kootenai River that are closely related to this proposal. The connections among the four projects are never fully described in any of the four proposals. There does not appear to be an overarching theme that knits these projects together in a unified strategic approach to restoration of this section of the Kootenai River. The only described process that would encourage coordination are meetings of the whole group working on these projects, that is biologists, engineers, and technical staff of all four projects. The proposals for these four projects seem to suggest disparate objectives for these meetings. For example, the nutrient addition project (199404900) proposal states "Project results will be summarized and presented at an annual meeting of the International Kootenai/y River Ecosystem Restoration Team (IKERT). This multidisciplinary group is comprised of project managers, scientists, and academicians who provide expertise, insight, guidance and adaptive management direction for the project." whereas the present proposal indicates that IKERT is an outreach team, implying less direct involvement with technical direction of the project. The extent to which these meetings achieve inter-project coordination was not discussed, and it appears that a more formal process to achieve coordination would be beneficial. A much more complete discussion of the relationship, interactions, etc. among these projects should have been included in all of the proposals dealing with the section of the Kootenai River in Idaho. 

A list of presumed limiting factors for white sturgeon is provided in the proposal. Identification of these limiting factors appears to be partially founded on research that has been conducted in the project area on this species and on best professional judgment. The proposal indicates that the critical limiting factor for sturgeon habitat is lack of appropriate spawning habitat, specifically, hard substrate on which fertilized eggs can attach. It is not clear that the information provided in the proposal supports this contention. Some of the research on sturgeon survival seems to suggest that lack of recruitment may be more influenced by mortality occurring after hatching rather than failure of the eggs to hatch. Very few fish are produced by the release of large numbers of fertilized eggs and free embryos into the river. In contrast, yearling sturgeon released to the river survive at a very high rate. This observation suggests a problem with habitat for very young fish may have a greater influence on recruitment than the lack of substrate for egg attachment. If the assumption is that good habitat for spawning also represents good habitat for young sturgeon, this point was not addressed or supported in the proposal. The proposal does acknowledge that there appears to be a survival bottleneck during the early rearing period and suggests that it may be due to reduced biological productivity in the river owing to sequestration of nutrients upstream, behind Libby Dam. No information is provided to verify that low productivity is the cause of this survival bottleneck. In fact, the high survival of juvenile sturgeon after age 1 suggests that sufficient food is available to support these fish; why not larvae and fry?

The RME program for this project does not appear to be monitoring nutrient levels, primary production, or invertebrate production in the river. The program that is monitoring these factors (199404900) is located in the Canyon Reach where sturgeon spawning and post larvae habitat is not being monitored. This type of information, in conjunction with data on the dietary habits of the young sturgeon, would be required to establish that the assumption that lack of food is causing high mortality of young sturgeon is correct. Some of this information is being collected as part of the Kootenai nutrient addition project, but the linkages between these projects is not described. Additional work on the factors limiting sturgeon recruitment is clearly needed and should be a focus of the RME effort associated with this project. 

Many of the proposed habitat actions are focused more broadly on restoring the ecological health of the project reach rather than specifically addressing factors thought to impact sturgeon. Actions to restore bank stability, riparian vegetation, wetland habitats, etc. are all likely to make contributions to improved aquatic habitat. But it is difficult to determine whether or not these planned projects are in the most advantageous location to affect responses by the focal species. Some additional information on the factors limiting the productivity of burbot and the various salmonid species that are intended to benefit from this project could have helped to verify that the proposed actions are located in an appropriate location to benefit these fishes.

The effects of non-natives species, especially brown trout and Didymo, deserve additional consideration.

4. Deliverables, Work Elements, Metrics, and Methods

This proposal covers a large number of very ambitious, and expensive, work elements and deliverables. Elements related to the completion and maintenance of project elements that have already been initiated or completed are described in sufficient detail. But the activities associated with the projects slated for phases 2 and 3 would have benefited from a more thorough discussion of what will be required to move these projects to execution. A considerable amount of general engineering detail is provided in the proposal, especially regarding the location of specific project elements. However, description of these phase 2 and 3 projects indicates that feasibility assessment and design have yet to be completed. It is not clear what the feasibility assessment entails. Is this primarily obtaining landowner cooperation and environmental permits? Or is there still some uncertainty that the projects can be executed as designed? Technical review of these proposed projects is difficult without understanding what must be accomplished prior to beginning construction. It is also difficult to understand how accurate estimates of project costs could be generated prior to the completion of the feasibility assessment and project design. Submitting each project as an individual proposal, once the planning, design, and feasibility steps have been completed might be more efficient for moving projects in this program through the review process.

Several other statements in the proposal require clarification. 

  • The sponsors state that they will “complete a feasibility study, 35% design, and final design to place suitable substrate at select locations in the Shorty’s Island/Meander Reach area of the Kootenai River where white sturgeon are currently spawning.” It would be helpful to obtain information on how impacts to the existing spawning substrate will be avoided during the execution of construction for this project. 

  • The proposal further states, “Specifically, the height, location and composition of the substrate beds is designed to avoid inundation by sand dunes on the river bottom, sedimentation during the spawning season, or infilling of interstitial spaces by sediments.” It would be useful to obtain further information on how reliable the models are that were used in developing this design.

  • The sponsors state, “This deliverable includes implementation of approximately 12 habitat restoration projects in the braided and straight reaches which are designed to provide specific ecological benefits to Kootenai sturgeon.” It is not clear why so much emphasis is placed on riparian habitat when the benefits of riparian conditions to sturgeon rearing has been questioned (McAdam et al 2005). If the riparian components of this project are intended to primarily benefit species other than sturgeon, this fact should have been discussed in the proposal.

  • The proposal indicates that in work element P3-2: “Implement Phase 3 projects in the meander reaches.” However, planning for this project element is incomplete, so implementation appears to be premature. 

  • The proposal indicates that the development and calibration model being used to support the engineering designs for the substrate placement at Shorty’s Reach is only 23% complete. Is it premature to rely on this tool for the design of a major engineering project?

The sponsors should be complimented for their successful outreach and educational efforts. However, if projects start to unravel because of unexpected changes that may affect ecosystem recovery, for example outlier low or high flows, working relationships between parties may be strained and an adaptive management plan that allows for contingency planning is crucial.

4a. Specific comments on protocols and methods described in MonitoringMethods.org

The details on the overall RME program for the suite of projects planned for the Kootenai River will apparently be provided in an adaptive management plan currently under development. The information provided in the proposal was not sufficiently detailed to enable review. Assessment of the RME effort for this project, therefore, should occur once the adaptive management plan is complete.

Several monitoring efforts related to this project were included in the proposal. Post-project implementation of habitat conditions is planned and links are provided to some of the monitoring methods proposed for use in this effort. However, the descriptions of the methods at this site were often incomplete.

There was no indication in the proposal that assessments of water quality and biological productivity of the river were to be monitored. As noted above, the assumption that sequestration of nutrients above Libby Dam is limiting productivity of white sturgeon has not been well documented, at least based on the information provided in the proposal. As noted earlier, some monitoring and research relevant to this project may be occurring as a part of the nutrient enhancement effort being conducted by the tribe, but insufficient information about RME associated with the nutrient project was provided in this proposal (nor were project linkages adequately described). In addition, the monitoring and evaluation design does not seem to have a sound statistical framework. 

There was no discussion about toxic compounds in the river and what influence they may be having on the health of this ecosystem. However, the proposal did indicate that there were industrial sites adjacent to the river that may be contaminated and that the Bonner’s Ferry waste water treatment plant discharges to the river within the study reach. These factors suggest that toxic chemicals in the river could be an issue and this should be investigated as a part of the monitoring program. The proposal indicated that procedures for monitoring at scales larger than the individual project will be included in the subbasin-scale adaptive management plan. As noted above, this plan should be reviewed as part of this proposal.

The discussion of critical uncertainties research in the proposal states: “This deliverable is to conduct limited critical uncertainties research that is necessary to identify and/or refine design criteria for the KRHRP Phase 2 or 3 projects or otherwise specifically support design or implementation of the projects.” and is conducted to “support Obj 2 i.e. Restore and maintain Kootenai River habitat conditions that support all life stages of native Kootenai subbasin focal fish species (i.e., all life stages of burbot, kokanee, redband trout, westslope cutthroat trout, and bull trout.” This is perhaps the most important deliverable for adaptive management, but emphasis on it seems to be limited. Surprisingly, the contention that survival of eggs and early fry is a key limiting factor for sturgeon recruitment did not seem to be reflected in the priorities of the RME program. Will additional early life history research be included as part of the monitoring effort? Using fin ray geochemistry to assess historical white sturgeon life history movements in the Kootenai River is indicated as a pilot study under critical uncertainties. The ISRP/ISAB expressed concern about the reliability of this technique in their recent tagging report. The project sponsors should consider these concerns prior to initiating this pilot study.

References

 McAdam, S.O.2011 Effects of substrate condition on habitat use and survival by white sturgeon (Acipenser transmontanus) larvae and potential implication for recruitment Can. J. Fish. Aquat. Sci. 68: 812–822

 McAdam, S.O., Walters, C.J., and Nistor, C. 2005. Linkages between white sturgeon recruitment and altered bed substrates in the Nechako River, Canada. Trans. Am. Fish. Soc. 134(6): 1448-1456.

 Bevelheimer, M.S. 2002. A bioenergetics model for white sturgeon Acipenser transmontanus: assessing differences in growth and reproduction among Snake River reaches. J Appl Ichthyol. 18:550-6.

 van Poorten BT, McAdam SO. 2010. Estimating differences in growth and metabolism in two spatially segregated groups of Columbia River white sturgeon using a field-based bioenergetics model. Open Fish Sci J 3:132-141.

Modified by Dal Marsters on 4/16/2012 10:43:55 PM.

Modified by Dal Marsters on 4/16/2012 10:44:20 PM.
Documentation Links:
  • Proponent Response (3/7/2012)
Proponent Response:

The ISRP requested responses to five specific points related to the Kootenai River Habitat Restoration Project 200200200:

  1. More detail on the feasibility assessments and design activities for Phase 2 and 3 projects should be presented.
  2. A draft of the KRHRP monitoring and adaptive management plan should be provided.
  3. Ten recruitment failure hypotheses are listed in the proposal.  Identify which of these hypotheses have been tested and what conclusions have been reached.
  4. Summarize the history and results from the spill tests resulting from the suite by the Center for Biological Diversity (CBD) in 2003 that concerned the RPA in the 2000 Biological Opinion and the designation of Kootenai sturgeon critical habitat.
  5. There are three other projects on the Kootenai River that are closely related to this proposal.  Describe how this project connects with these projects.

In addition, the ISRP presented a range of comments and some additional questions related to the following major proposal components:

  1. Purpose: Significance to regional programs, technical background, and objectives
  2. History: Accomplishments, results, and adaptive management (ISRP review of results)
  3. Project relationships, emerging limiting factors, and tailor questions for type of work (hatchery, RME, tagging)
  4. Deliverables, work elements, metrics, and methods (and specific comments on protocols and methods described in MonitoringMethods.org)

The Kootenai Tribe of Idaho (Kootenai Tribe) wishes to thank the ISRP for their review of this project and for the opportunity to provide additional information and clarification about the project specifics.  Our response generally follow’s the format of the ISRP comments.  In some cases we’ve combined some of the topics raised by the ISRP in a single response in the hope that it will facilitate clear communication and understanding.  

I.  More detail on the feasibility assessments and design activities for Phase 2 and 3 projects should be presented.

The ISRP reviewers asked for additional detail on the feasibility assessment and design activities associated with the Phase 2 and Phase 3 projects.  The Tribe has developed a robust and efficient process, which incorporates multiple levels of review, to move from identification of limiting factors and restoration strategies, to sequential stages of design, and to implementation.  The process emphasizes a deliberate, measured and adaptive approach to design and implementation of the Kootenai River Habitat Restoration Program.  Following is a description of the activities and deliverables associated with each step of the process. 

1.  Kootenai River Habitat Restoration Program Master Plan, limiting factors and restoration strategies

In their comments on the Kootenai River Habitat Restoration Program (KRHRP) the ISRP reviewers express concern that the KRHRP is attempting to proceed without a clear identification of limiting factors or specific desired population objectives.  We wanted to provide some clarification in this regard as it is critical to understanding the proposed KRHRP, Phase 2 and 3 projects, and the overall approach to design and implementation. 

As described in the proposal, in 2008 the Kootenai Tribe began efforts to develop a Master Plan for the KRHRP (please see history of efforts leading up to the Master Plan in the proposal).  The master planning work, and efforts that lead to the Master Plan, were initially focused solely on designing a project that could provide physical habitat conditions consistent with the biological attributes for Kootenai River white sturgeon identified in the 2006 Libby Dam Biological Opinion (USFWS 2006).  As the master planning effort progressed, the participants strongly emphasized the need to adopt a broader ecosystem-based approach that incorporated habitat not only for all life stages of Kootenai sturgeon, but also addressed other native fish populations and ecosystem functions.  Additionally, it became increasingly clear that designing a project to address only one life stage of Kootenai sturgeon posed potentially deleterious implications for the habitat used by many other aquatic species, and could in fact result in declines of overall ecosystem function.  

Ecological restoration can be defined as the process of assisting the recovery of an ecosystem that has been degraded, damaged or destroyed (SER 2004).  A restored ecosystem can be defined as one containing sufficient biotic (living) and abiotic (non-living) resources to continue its development without further assistance and that will sustain itself structurally and functionally, demonstrate resilience to normal ranges of disturbance and interact with contiguous ecosystems in terms of biotic and abiotic flows and cultural interactions (SER 2004).  The KRHRP Master Plan is based on a restoration approach that emphasizes a holistic, multidisciplinary approach to evaluating and restoring ecosystem function and structure.  The concepts of ecosystem function and structure are closely intertwined and both include abiotic and biotic elements and processes. 

This philosophy emphasizes the need for improving or re-establishing both the structural components and the functions of the river ecosystem to restore the conditions necessary to create and maintain habitat benefiting a range of species in dynamic environments.  Species are often the most noticeable symptom of ecosystem decline, but the holistic ecosystem approach to restoration focuses on system-wide stressors and interactions that are responsible for those declines.  Within the KRHRP Master Plan, these system-wide stressors are referred to as limiting factors.  By identifying combinations of restoration strategies to address multiple limiting factors, we recognize that an ecosystem is made up of a diverse set of interacting components such that no single restoration action will restore the ecosystem.

This philosophy is consistent with the NPCC’s Fish and Wildlife Program’s Habitat Strategies, one of which states, ‘Restore Ecosystems, Not Just Single Species’.  This strategy recognizes that increasing the abundance of single populations may not, by itself, result in long-term recovery and that restoration efforts must focus on restoring habitats and developing ecosystem conditions and functions that will allow for expanding and maintaining diversity within and among species.  Taking this approach to restoration will help sustain a system of robust populations in the face of environmental variation (NPCC 2009).

A central premise of an ecosystem-based approach to restoration is that restoration should create conditions that will sustain natural processes and prevent the system’s further degradation while simultaneously conserving its native plants and animals.  Given that ecosystems are in constant flux and that there is no single correct condition, this philosophy accepts the possibility of a number of responses, trajectories or end points for restoration actions.  However, in a restored system, this flux would happen within the bounds of a most probable state (Leopold 2004).  This concept, based on observations of unimpeded ecosystem processes, suggests that riverine systems achieve a relatively stable form over time based on a balanced distribution of energy throughout the system.  Within the most probable state, constant change would be the norm, driven by natural ecosystem processes such as flows and other stochastic events. 

Thus, restoration planning at the ecosystem scale requires integrating a “toolbox” of restoration strategies and techniques within an adaptive framework that allow strategies to shift according to ecosystem response.  The techniques and strategies included in the KRHRP include both active and passive approaches to allow natural river processes to create the biotic and abiotic components of habitat.  Active techniques involve direct structural modifications to the river, its floodplain or infrastructures (i.e. channel realignment, levee removal, instream habitat structures).  Passive techniques rely on the river to do the work (flow augmentation, changes in land use) (Stanford et al. 1996).  This type of integrated approach is necessary in altered ecosystems where allowing natural processes alone to create habitat or other desired functions may not be feasible given limiting factors, social and economic factors or necessary timeframes for recovery.  For example, when changes in the ecosystem have altered hydrologic inputs and sediment loads it may not be reasonable to expect pre-disturbance channel dimensions and habitat to be created and maintained by current processes.  This approach also recognizes that a failure to account for human interactions within restored systems is both unrealistic and undesirable for their long-term sustainability. 

This approach integrates a range of disciplines and schools of thought regarding river restoration, including ecosystem theory applied to restoration (Frissell et al. 1993; Stanford 1996 and Kondolf et al. 2006) and reference or analog approaches through evaluations of historical conditions including use of reference sites and applied models describing geomorphology—flow—sediment-transport relationships (SER 2005; Rosgen 1996).  The Tribe does not subscribe solely to any one of these approaches, but recognizes that each has value and that they collectively form a conceptual toolbox that makes it possible to contemplate ecosystem restoration at the scale of the KRHRP.

Consistent with this overall restoration philosophy, the Tribe identified four goals in the KRHRP Master Plan (KTOI 2009).  These goals addressed river morphology, riparian vegetation, aquatic habitat and river stewardship:

  • Morphology.  Restore physical habitat by reducing the negative effects to river and floodplain ecological processes caused by river response to the altered landscape.
  • Riparian vegetation.  Restore native vegetation by establishing stream bank and floodplain conditions that sustain plant community development processes.
  • Aquatic habitat.  Restore aquatic habitat conditions that support all life stages of native fish and promote sustainable populations.
  • River stewardship.  Create opportunities for river and floodplain stewardship in the community.

These goals support several stated objectives in the Kootenai Subbasin Plan that relate to habitat (KTOI and MFWP 2004).  Within the Kootenai Subbasin Plan, objectives were organized according to habitat types (mainstem, tributaries, and reservoir), focal species (bull trout, sturgeon, burbot, kokanee, redband and westslope cutthroat trout), and biomes (regulated mainstem, wetland, riparian, grassland/shrub, xeric forest, and mesic forest).  For each of these components, several objectives were identified and numbered, for example, Objective M1 is Mainstem Objective 1.  Table 1 provides an example of the relationship of KRHRP goals to the Kootenai River Subbasin Plan objectives. 

Table 1.  Kootenai River Habitat Restoration Program goal and related Kootenai River Subbasin Plan habitat objective.  

KRHRP Program Goal

Supporting Subbasin Plan Habitat Objective

1. Morphology. Restore physical habitat by reducing the negative effects to river and floodplain ecological processes caused by river response to the altered landscape.

M6 (Mainstem Kootenai River). Improve channel stability to a level equivalent to the QHA-generated, channel stability habitat restoration scores of reference streams, assuming that such levels will support sustainable population levels of focal species that function naturally and may be capable of supporting appropriate forms of human use.

2. Riparian Vegetation. Restore native vegetation by establishing stream bank and floodplain conditions that sustain plant community development processes. 

T2 (Tributary). Restore riparian habitats to levels equivalent to the QHA-generated riparian condition habitat restoration scores of reference streams. 

RP1 (Riparian). Restore riparian vegetation communities on 10% of the riparian acres in those subunits for which the Floodplain Vegetation Index/Vegetation Distribution Intensity Index in the TBA spreadsheet tool is < a value of 8, consistent with current or future management and mitigation plans. 

RP4. Restore riparian vegetation communities on 10% of the riparian acres in those subunits for which the Floodplain Vegetation Index/Vegetation Distribution Intensity Index in the TBA spreadsheet tool is > a value of 8, consistent with current or future management and mitigation plans. 

Most Grassland/shrub, Xeric Forest and Mesic Forest Objectives in the Subbasin Plan also support this goal. 

3. Aquatic Habitat. Restore aquatic habitat conditions that support all life stages of native fish, and promote sustainable populations.

M2.  Improve riparian function and complexity of mainstem riparian habitat to levels that support or contribute to sustainable population levels of focal species that function naturally and may be capable of supporting appropriate forms of human use.

M5. Improve habitat diversity to levels equivalent to the QHA-generated habitat diversity habitat restoration scores, and habitat diversity conditions based on ecological primary literature and possible references rivers.

T1 (Tributary). Protect and maintain prime, functioning tributary habitat (identified as Class 1 in QHA analysis)

T6a. Protect habitat diversity in Class 1 streams and reaches.

T6b. Improve habitat diversity to a level equivalent to the QHA-generated habitat diversity scores of reference streams.

T7b. Determine opportunities for altered hydro operations to remove delta blockages from tributary streams.

T8. Restore and provide passage to migratory fish by removing potential man-caused barriers, i.e. impassable culverts, hydraulic headcuts, water diversion blockages, landslides, and impassable deltas.

WST1 (White Sturgeon), BT5 (Bull Trout), and KOK1 (Kokanee). Restore primary, secondary, and tertiary productivity rates and nutrient values downstream from Libby Dam to pre-dam condition (equal to those of inflows into Koocanusa Reservoir, corrected for downstream lateral input).

KOK1 (Kokanee). Restore primary, secondary, and tertiary productivity rates and values downstream from Libby Dam to pre-dam condition (equal to those of inflows into Koocanusa Reservoir).

4. River Stewardship.  Create opportunities for river and floodplain stewardship in the community.

RP3. Secure management rights and implement management agreements to conserve, maintain and restore 10% in those subunits for which the Floodplain Vegetation Index in the TBA spreadsheet tool is > a value of 7, consistent with current or future management and mitigation plans.

RP5. Monitor and treat an average of 10% of acres in those subunits for which the Exotic Vegetation Index in the TBA spreadsheet tool is > a value of 6, consistent with current and future management and mitigation plans.

Most Grassland/shrub, Xeric Forest and Mesic Forest Objectives support this goal.


KRHRP Program Goal

Supporting Subbasin Plan Habitat Objective

1. Morphology. Restore physical habitat by reducing the negative effects to river and floodplain ecological processes caused by river response to the altered landscape.

M6 (Mainstem Kootenai River). Improve channel stability to a level equivalent to the QHA-generated, channel stability habitat restoration scores of reference streams, assuming that such levels will support sustainable population levels of focal species that function naturally and may be capable of supporting appropriate forms of human use.

2. Riparian Vegetation. Restore native vegetation by establishing stream bank and floodplain conditions that sustain plant community development processes. 

T2 (Tributary). Restore riparian habitats to levels equivalent to the QHA-generated riparian condition habitat restoration scores of reference streams. 

RP1 (Riparian). Restore riparian vegetation communities on 10% of the riparian acres in those subunits for which the Floodplain Vegetation Index/Vegetation Distribution Intensity Index in the TBA spreadsheet tool is < a value of 8, consistent with current or future management and mitigation plans. 

RP4. Restore riparian vegetation communities on 10% of the riparian acres in those subunits for which the Floodplain Vegetation Index/Vegetation Distribution Intensity Index in the TBA spreadsheet tool is > a value of 8, consistent with current or future management and mitigation plans. 

Most Grassland/shrub, Xeric Forest and Mesic Forest Objectives in the Subbasin Plan also support this goal. 

3. Aquatic Habitat. Restore aquatic habitat conditions that support all life stages of native fish, and promote sustainable populations.

M2.  Improve riparian function and complexity of mainstem riparian habitat to levels that support or contribute to sustainable population levels of focal species that function naturally and may be capable of supporting appropriate forms of human use.

M5. Improve habitat diversity to levels equivalent to the QHA-generated habitat diversity habitat restoration scores, and habitat diversity conditions based on ecological primary literature and possible references rivers.

T1 (Tributary). Protect and maintain prime, functioning tributary habitat (identified as Class 1 in QHA analysis)

T6a. Protect habitat diversity in Class 1 streams and reaches.

T6b. Improve habitat diversity to a level equivalent to the QHA-generated habitat diversity scores of reference streams.

T7b. Determine opportunities for altered hydro operations to remove delta blockages from tributary streams.

T8. Restore and provide passage to migratory fish by removing potential man-caused barriers, i.e. impassable culverts, hydraulic headcuts, water diversion blockages, landslides, and impassable deltas.

WST1 (White Sturgeon), BT5 (Bull Trout), and KOK1 (Kokanee). Restore primary, secondary, and tertiary productivity rates and nutrient values downstream from Libby Dam to pre-dam condition (equal to those of inflows into Koocanusa Reservoir, corrected for downstream lateral input).

KOK1 (Kokanee). Restore primary, secondary, and tertiary productivity rates and values downstream from Libby Dam to pre-dam condition (equal to those of inflows into Koocanusa Reservoir).

4. River Stewardship.  Create opportunities for river and floodplain stewardship in the community.

RP3. Secure management rights and implement management agreements to conserve, maintain and restore 10% in those subunits for which the Floodplain Vegetation Index in the TBA spreadsheet tool is > a value of 7, consistent with current or future management and mitigation plans.

RP5. Monitor and treat an average of 10% of acres in those subunits for which the Exotic Vegetation Index in the TBA spreadsheet tool is > a value of 6, consistent with current and future management and mitigation plans.

Most Grassland/shrub, Xeric Forest and Mesic Forest Objectives support this goal.

In the Master Plan, as was the case in the subbasin planning process, native focal fish species (Kootenai River white sturgeon, burbot, bull trout, interior redband trout kokanee, and westslope cutthroat trout) were selected to serve as indicators for the broader range of native aquatic species that are part of the Kootenai River ecosystem.  Although not specifically included in the table above, objectives identified for the aquatic focal species in the Kootenai River Subbasin Plan are also largely addressed by the four project goals. 

In developing the Master Plan we identified a suite of limiting factors associated with three of the goals identified above (i.e., morphology, riparian vegetation, and aquatic habitat).  In addition, we identified a fourth category related to river stewardship and other management issues, which was summarized as “river and floodplain management constraints”.  In the context of the KRHRP, limiting factors are defined as physical, biological, and ecological conditions within the project area that: 1) limit the ability of the ecosystem to sustain diverse native plant and animal populations, and to accommodate natural disturbances; 2) limit the quality or availability of habitat that supports all life stages of endangered Kootenai sturgeon and other focal species; and 3) limit the ability of the ecosystem to sustain the local tribal culture, subsistence needs, and the economy.  Limiting factors can be addressed by active restoration or changes in management.  In contrast, constraints are components like Libby Dam, roads, bridges and other infrastructure that cannot be changed by management or active restoration, but must be considered during the design process. 

A summary of the limiting factors for constraints, morphology, riparian habitat and aquatic habitat from the Master Plan was presented in our November 2011 proposal.  Additional detailed discussion of each limiting factors is presented in the KRHRP Master Plan (KTOI 2009).  An abbreviated list is provided here:

  • Constraints from river and floodplain management
    • Dam controlled flow regime
    • Dam controlled sediment regime
    • Dam controlled thermal regime
    • Dam controlled nutrient regime
    • Bank armoring
    • Levees and diking districts
    • Transportation corridors
    • Floodplain land use   
    • Backwater influence from Kootenay Lake
  • Limiting factors for morphology
    • River response to altered hydraulics
    • River response to altered sediment-transport
    • Loss of channel and floodplain connection
    • Reduced channel boundary roughness and bank erosion
  • Limiting factors for riparian vegetation
    • Lack of surfaces that support riparian vegetation recruitment
    • Lack of outer bank vegetation
    • Frequent scour and deposition of floodplain surfaces
    • Altered hydroperiod
    • Invasive plant species
    • Lack of native plant diversity and seed sources
    • Lack of nutrient sources for primary productivity
    • Altered carbon balance
  • Limiting factors for aquatic habitat
    • Insufficient depth for Kootenai sturgeon migration (BiOp)
    • Insufficient velocity for Kootenai sturgeon spawning sturgeon spawning, incubation, and early life stages (BiOp)
    • Lack of coarse substrate for egg attachment (BiOp)
    • Lack of cover for juvenile fish
    • Lack of pool-riffle complexity
    • Simplified food web from lack of nutrients
    • Insufficient pool frequency
    • Lack of fish passage into tributaries
    • Lack of off-channel habitat for rearing, primary, and secondary production and species diversity
    • Altered water quality

The Master Plan presented a synthesis of existing information (as of 2009) related to each of the identified limiting factors.  As part of the ongoing feasibility analysis and design processes associated with each individual KRHRP project, this information is being continually updated and improved based on new data and information.  Based on the analysis of limiting factors presented in the KRHRP Master Plan, restoration strategies for each reach of the river (i.e., the broad approaches to habitat restoration that will be used in each project reach) were identified.  Each restoration strategy is described in terms of how the river channel, banks and floodplain would need to be modified in a reach to overcome limiting factors given specific conditions and constraints that are present.  The Master Plan presented a “toolbox” of specific restoration treatments, i.e., actionable concepts that support a restoration strategy to address the limiting factors and conditions specific to each of the river reaches addressed by the KRHRP (i.e., Braided Reach 1 and 2, Straight Reach and Meander Reach 1 and 2).

For each river reach, the capacity of the individual restoration treatments to address limiting factors associated with that reach was also assessed with the goal of combining treatments in the final design process that addressed as many limiting factors as possible.  From this information a range of conceptual implementation scenarios was derived for each river reach that quantified varying levels of restoration effort.  To develop these implementation scenarios, data about limiting factors and other natural resource components were used to create maps that illustrated a range of spatial extents for which a habitat action could be applied to address the limiting factors in that reach using a specific set of criteria.  These implementation scenarios provided a framework for future design of restoration projects by helping to prioritize where specific restoration actions should occur and a way to assess the relative benefits of implementing actions at different scales. 

Table 2 summarizes the limiting factors, strategies, quantifiable objectives and metrics developed in the Master Plan and presents them in relationship to the four KRHRP goals (KTOI 2009).  The Tribe is proud of the fact that the KRHRP Master Plan is presented as case study in Introduction to Restoration Ecology by Evelyn A. Howell, John A. Harrington and Stephen B. Glass (Howell et al. 2011).  The KRHRP 2009 Master Plan is posted on the Tribe’s web site at: http://www.restoringthekootenai.org/habitatRestoration/masterPlan/.

Table 2. Limiting factors, strategies, quantifiable objectives and metrics by the four KRHRP Master Plan goals. 

Limiting Factors/ Constraints

Restoration Strategy Components

Quantifiable Objectives 1

Metrics

Morphology

River and floodplain response to altered flow regime and altered hydraulics

Establish channel dimensions that are sustainable given the morphological setting and governing flow and sediment regimes.

Construct a meandering gravel-bed channel with side channels in the Braided Reaches.

 

Construct a confined gravel-bed channel in the Straight Reach.

 

Excavate floodplain adjacent to the channel in the Meander Reaches.

  • Channel width
  • Channel depth
  • Channel slope
  • Particle size distribution

River and floodplain response to altered sediment supply and sediment transport conditions

Gradually reduce sediment supply and transport competence in a downstream direction in order to promote deposition of sediment on the floodplain in the Braided Reaches and reduce deposition of sediment on the channel bed in downstream reaches.

Provide floodplain surfaces in the Braided and Straight Reaches that will increasingly store sediment over time.

 

Provide river and floodplain sediment transport conditions in the Braided and Straight Reaches that decrease sediment deposition in the channel and promote deposition of sediment on the floodplains.

  • Change in volume and area of depositional surfaces
  • Particle size distribution
  • Scour and fill depth on point bars
  • Channel width
  • Channel depth

Loss of floodplain connection

Establish channel and floodplain connection at mean annual peak flow where feasible given constraints from river and floodplain management.

In the Meander, Braided and Straight Reaches, increase acres of new floodplain surfaces at elevations that correspond to river stage between 20,000 and 30,000 cfs.

  • Channel profile
  • Bank height ratio
  • Observations of hydrologic connectivity

Accelerated bank erosion and reduced boundary roughness

Establish bank vegetation.

Increase channel roughness.

Within identified bank treatment areas, lateral bank migration is 0 ft per year for first five years while vegetation is becoming established.

 

Within identified bank treatment areas, less than 10 percent of bank length moves laterally less than 1 ft between years 5 and 10.

 

Within identified bank treatment areas, less than 30 percent of bank length moves laterally less than 1 ft between years 10 and 20.

  • BEHI ratings
  • Bank profiles
  • Bank erosion rates

 

Riparian vegetation

Lack of surfaces that support riparian recruitment

Increase floodplain areas with suitable substrate and elevation relative to the water table in order to support riparian vegetation recruitment and establishment.

In Braided Reaches, Increase acres of new floodplain surfaces by > 50 acres.

 

In Meander Reach, achieve an overall increase in acres of floodplain that has hydrology in the rooting zone sufficient to support cottonwoods, willows and hydrophytic vegetation.

  • Hydrologic connectivity
  • Groundwater depth
  • Canopy cover of plants
  • Area and stability of depositional surfaces

Lack of outer bank vegetation

Establish bank vegetation.

Streambank canopy cover will reach 30-50 percent between years 5-15 and >50 percent after 15 years for treated areas.

  • Canopy cover

Frequent scour/deposition of floodplain surfaces

Increase stability/longevity of floodplain surfaces.

Islands and point bars continue to grow and develop vegetation per designs for specific projects.

  • Area of depositional features and change in position over time

Altered hydroperiod

Increase floodplain areas with appropriate elevation ranges relative to the water table to support native tree and shrub species.

Increase in acres of floodplain connected to the water table between 20,000 and 30,000 cfs as noted by reach.

  • Groundwater depth
  • Wetland indicator status of plant species

Invasive weeds

Reduce weed cover so weeds do not limit recruitment and establishment of native plant species.

Weed canopy cover is less than 10 percent by year five.

  • Canopy cover invasive species
  • Weed mapping

Lack of native seed sources

Establish nodes of diverse, native vegetation within the Straight Reach and Meander Reaches.

Native vegetation is establishing on developing floodplain surfaces and river banks according to project-specific designs.

  • Native plant species canopy cover and diversity as measured by number of species by life form

Lack of nutrient sources for primary productivity and limited carbon storage (reduced primary productivity).

Increase amount and diversity of native vegetation and wetlands within the Meander Reaches.

Native vegetation is establishing on developing floodplain surfaces and river banks according to project-specific designs.  Evidence of increased primary production.

  • Combination of vegetation metrics and other metrics from KTOI Operation Loss studies

Aquatic habitat

Insufficient depth for KRWS migration preference

Provide depth conditions for normal KRWS migration and spawning behavior in KRWS migration reaches.

Provide intermittent depths of 16.5 to 23 ft or greater in 60 percent of the area of rocky substrate from RM 152 to RM157 during peak augmentation flows.

  • Channel depth
  • BiOp monitoring completed by others

Insufficient velocity for KRWS spawning preference

Provide velocity conditions for KRWS spawning and embryo/free-embryo incubation and rearing in KRWS spawning reaches.

Provide velocities of 3.3 ft/s and greater in approximately 60 percent of the area of rocky substrate from RM 152 to RM157 during post-peak augmentation flows.

  • Flow velocity
  • BiOp monitoring completed by others

Lack of coarse substrate for KRWS egg attachment

Provide substrate conditions for KRWS embryo/free-embryo incubation and rearing in KRWS spawning reaches.

Coarse substrate suitable for sturgeon spawning has been placed and is not buried by sediments at the time of spawning in the Meander Reaches at the locations of known spawning behavior, general corresponding with pool tailout locations in Meander Reach 1.

  • Particle size measurements and distribution
  • BiOp monitoring completed by others

Lack of cover for juvenile fish

Increase in-stream and bank cover by constructing in-stream structures and establishing bank vegetation.

Enhance vegetated bank cover in > 20,000 linear ft within the Braided Reaches, and within the Straight and Meander Reaches according to project-specific designs.

  • Canopy cover of bank vegetation and density of instream cover

Lack of pool-riffle complexity

Increase hydraulic habitat complexity by establishing ratios of pool and riffle habitat that are appropriate for the morphological setting.

Establish increased pool/glide habitat and increased riffle/run habitat in all reaches according to project-specific designs.

  • Pool and riffle habitat lengths by reach

Simplified food web from lack of nutrients

Increase nutrient availability.

Reference nutrient addition program and reference other goals/objectives aimed at increasing ecosystem productivity.

  • Combination of metrics and other KTOI M&E metrics from Operational Loss Assessment

Insufficient pool frequency

Establish pool frequency that is appropriate for the morphological setting.

Establish pool frequency of one pool per unit length corresponding to 5 to 7 bankfull widths.

  • Pool spacing

Lack of fish passage into tributaries

Establish fish passage at known barriers on tributaries within the project area.

Remove fish passage barriers on tributaries.

  • Depth and velocity criteria for target species

Lack of off-channel habitat for rearing

Increase availability of off-channel habitat for native aquatic species.

Increase acres of off-channel habitat that is connected to the mainstem at 10-20,000 cfs. 

  • Area of off-channel habitat features
  • Observations in off-channel areas

Altered water quality

Identify and reduce point source pollutant inputs into Kootenai River and tributaries.

Identify specific opportunities to reduce pollutant inputs within site-specific designs.

  • Turbidity
  • Chemical analysis

River stewardship

Dam controlled flow, sediment and thermal regimes

Develop habitat actions that are compatible with modified regimes and work with Libby Dam managers so operations support habitat restoration efforts.

Verify that coordination is happening.

  • Documented coordination

Floodplain grazing

Coordinate with landowners and grazing lessees to explore development of grazing management plans that allow floodplain vegetation to develop.

Grazing is controlled by riparian fencing to protect riparian buffer, and riparian vegetation does not exhibit signs of livestock grazing within project areas.

  • Documented coordination

Floodplain agriculture

Coordinate with landowners to explore the potential to modify or relocate agricultural operations in areas where habitat actions will occur.

Agricultural land use is separated from restoration projects through formal landowner agreements.

  • Documented coordination

Bank armoring

Coordinate with appropriate parties to maintain, modify or remove bank armoring to support channel, riparian and floodplain ecological processes according to specific habitat actions.

Where possible as part of project designs, hard bank armor will be replaced with vegetation-based bank treatments.

  • Documented coordination

Levees

Coordinate with diking districts and other effected parties to maintain, modify or remove levees to support channel, riparian and floodplain ecological processes according to specific habitat actions.

Verify that coordination is happening.

  • Documented coordination

Railroad encroachment on river and floodplain

Develop habitat actions that are compatible with existing infrastructure; and work with owners to mitigate for potential impacts to infrastructure from project actions.

Maintain a buffer between the river and the railroad through coordination with the railroads.

  • Documented coordination

Floodplain draining/pumping

Work with diking districts, NRCS, SCD, and landowners as appropriate to Identify areas where floodplain draining and pumping can be modified to restore floodplain hydrology.

Coordinate with diking districts.

  • Documented coordination

Floodplain tilling/grading

Work with NRSC, SCD, and landowners as appropriate to identify areas where microtopography and roughness can be restored to floodplain surfaces.

Agricultural land use is separated from restoration projects through formal landowner agreements.

  • Documented coordination

Bridge encroachment on river and floodplain

Design habitat actions that are compatible with bridge infrastructure and work with the Idaho Department of Transportation to mitigate for potential impacts to infrastructure from project actions.

Coordinate with transportation departments.

  • Documented coordination

Backwater influence from Kootenay Lake

Work with BC and other entities to explore and identify potential modifications to Kootenay Lake level management and design habitat actions that would complement those potential changes to Lake level management.

Reduce the backwater influence by lowering the backwater elevation during high flows as possible through coordination with British Columbia.

  • Backwater elevation

Urban development adjacent to river

Design habitat actions that do not place urban infrastructure at risk, and create riparian buffers to separate city from river where possible by working with Bonners Ferry and landowners.

Increase riparian buffers along river frontage based on results of coordinating with landowners.

  • Documented coordination
  • Length of riparian buffer

Removal of riparian buffer

Work with NRSC, SCD, and landowners as appropriate to restore native vegetation along river banks.

Establish at least 30 percent canopy cover of native woody plants within identified buffer areas within 10 years.  Establish at least 80 percent canopy cover within 20 years.

Reduce weed canopy cover to less than 10 percent within identified buffer areas within 5 years.

  • Proportional abundance of native woody species
  • Canopy cover
  • Weed mapping

1 Where thresholds are not specified, they are indicated with an ‘X’ and will be developed during subsequent project design phases.

In the ISRP reviewers’ response to the KRHRP 2011 proposal, the reviewers comment that it would be helpful if the project objectives were more quantitative and included measures of incremental success.  The ISRP also suggested that objectives should include both habitat and demographic targets and be closely linked to the RME efforts. 

In summary the objectives identified in the 2011 proposal for the KRHRP project are to:

  • Objective 1.  Restore and maintain Kootenai River habitat conditions that support all life stages of Endangered Species Act listed Kootenai River white sturgeon.  Working within the constraints posed by construction and operation of Libby Dam and the backwater influence of Kootenay Lake, restore morphological, aquatic and riparian habitat conditions that support all life stages (i.e., embryo, free embryo, larva, age 0+ juvenile, non-reproductive adult, migrating adult, spawning adult) of Kootenai River white sturgeon.  Restore habitat conditions that address factors limiting recruitment and early life stage success and subsequent bottlenecks to successful self-sustaining populations of white sturgeon.  Restore a delisted white sturgeon population capable of supporting future Tribal Treaty subsistence and cultural harvest as well as recreational harvest. Restore habitat conditions that support long-term survival of Kootenai River white sturgeon.   
  • Objective 2.  Restore and maintain Kootenai River habitat conditions that support all life stages of native Kootenai subbasin focal fish species (burbot, westslope cutthroat trout, kokanee, ESA listed bull trout, interior redband trout, mountain whitefish, and other native fish).  Working within the constraints posed by construction and operation of Libby Dam and the backwater influence of Kootenay Lake, restore morphological, aquatic and riparian habitat conditions that support all life stages of burbot, westslope cutthroat trout, kokanee, ESA listed bull trout, interior redband trout, mountain whitefish, and other native fish.  Restore habitat conditions that address factors limiting all life stages of Kootenai River native fish populations.  Restore habitat conditions that support delisting of bull trout, successful reintroduction of native burbot and successful self-sustaining populations of other Kootenai River native fish populations.  Restore populations of Kootenai River native fish capable of supporting future Tribal Treaty subsistence and cultural harvest as well as recreational harvest.   

Quantitative objectives for the six project aquatic focal species are best described in terms of the recovery targets identified in the Kootenai River Subbasin Plan and in various recovery plans or in the other recovery guidance that has been developed for each species.  These various targets reflect best professional opinion and the current regional consensus. 

White sturgeon

The Recovery Criteria from the USFWS 1999 Recovery Plan for the Kootenai River Population of the White Sturgeon (criteria required for reclassification or downlisting to threatened status) (USFWS 2006, BiOp RPA 4a and 4b):

  1. Natural production of white sturgeon occurs in at least 3 different years of a 10-year period; a naturally produced year class is demonstrated when at least 20 juveniles from a year class are sampled at more than 1 year of age.
  2. The estimated white sturgeon population is stable or increasing and juveniles reared through a conservation aquaculture program are available to be added to the wild population each year for a 10-year period. Each of these year classes must be large enough to produce 24 to 120 sturgeon surviving to sexual maturity.

Additional guidance is found in the Kootenai Tribe’s Native Fish Conservation Aquaculture Master Plan.  Working criteria to guide development of conservation aquaculture program objectives for Kootenai sturgeon include the following targets (KTOI 2010):

  • Abundance.  A minimum adult population size of 2,500 (for downlisting) and a target adult population size of 8,000-10,000 (for delisting). 
  • Productivity.  Naturally-produced recruitment and juvenile population sizes sufficient to support the desired adult population size.  Stable or increasing trends in adult and juvenile numbers. Representative and stable size and age structure. 
  • Distribution.  Distribution and use of habitats throughout the majority of the historical range.  Breadth of distribution such that population is not vulnerable to any single human-caused catastrophic event (chemical spill for instance). 
  • Diversity.  Stable genetic diversity (including frequencies of common and rare alleles). Effective population sizes adequate to allow for normal genetic and evolutionary processes.  
  • Use.  Numbers (consistent with above) adequate to support significant subsistence harvests and recreational fishery uses. 

The Urgent and High Priority Aquatic Objectives for White Sturgeon (WST 2 and 3a) identified in the Kootenai Subbasin Plan (KTOI and MFWP 2004) are to:

  • Achieve an estimated white sturgeon population that is stable or increasing with juveniles reared through a conservation aquaculture program available to be added to the wild population each year for a 10-year period. 
  • Achieve natural production of white sturgeon in at least 3 different years of a 10-year period.  Prevent extinction, preserve genetic variability, and restore demographic viability of the Kootenai River white sturgeon population through the propagation and release of progeny produced from wild white sturgeon from the Kootenai River

Burbot

Urgent and High Priority Aquatic Objectives for Burbot (BUR 3a, BUR3b, and BUR4) identified in the Kootenai Subbasin Plan (KTOI and MFWP 2004), the Burbot Subcommittee of the Kootenai Valley Resource Initiative (KVRI 2005), and the Kootenai River Native Fish Conservation Aquaculture Master Plan (KTOI 2010) are to:

  • Achieve consistent natural recruitment in at least three different spawning areas with net recruitment and juvenile population size sufficient to support desired adult population size.
  • Achieve stable size and age distributions as determined by an upward trend in a 6-year moving average of population abundance.
  • Achieve a minimum number of 2,500 adults in the burbot population.
  • Produce and stock burbot at rates and frequencies to sustain a target population of 2,500 to 9,500 adults in the Kootenai River and South Arm of Kootenay Lake

Kokanee

Urgent and High Priority Aquatic Objective for Kokanee (KOK3) identified in the Kootenai Subbasin Plan (KTOI and MFWP 2004) are to:  

  • Document greater than 100 adult spawning kokanee in each tributary by 2020
  • Develop a multi-year average of 250 adult spawning kokanee in each tributary by 2030

Westslope Cutthroat

Urgent and High Priority Aquatic Objectives for Westslope Cutthroat (WCT1 and WCT2) identified in the Kootenai Subbasin Plan (KTOI and MFWP 2004) are to:  

  • Maintain or increase the total number of genetically pure local populations, and maintain the broad distribution of local populations in existing metapopulations
  • Achieve at least 5 genetically pure conservation populations (including British Columbia tributaries) with 50 adults in each of the subpopulations in Lake Koocanusa, Kootenai River and Kootenay Lake, with each of these conservation populations containing at least 500 adult westslope cutthroat trout.

Redband Trout

Urgent and High Priority Aquatic Objectives for Redband Trout (RBT1a and RBT2) identified in the Kootenai Subbasin Plan (KTOI and MFWP 2004) are to:

  • Maintain or increase the total number of genetically pure local populations.
  • Achieve a minimum of 2 genetically pure conservation populations, each containing at least 250 adult redband trout (including British Columbia tributaries). In Kootenai Subbasin redband trout populations that have subpopulations, subpopulations should contain at least 50 adult individuals to improve the probability of subpopulation persistence.

Bull Trout

Urgent and High Priority Aquatic Objectives for Bull Trout (BT2a and BT3) identified in the Kootenai Subbasin Plan (KTOI and MFWP 2004) and Bull Trout Recovery Criteria from 2002 USFWS Bull Trout Recovery Plan (Chapter 4, Kootenai River Recovery Unit) are to:

  • Achieve at least 5 local populations (including British Columbia tributaries) with 100 adults in each of the primary Lake Koocanusa and Kootenai River/Kootenay Lake core areas, with each of these primary core areas containing at least 1,000 adult bull trout.
  • Achieve an overall bull trout population trend in the Kootenai River Recovery Unit that is accepted, under contemporary standards of the time, to be stable or increasing, based on at least 10 years of monitoring data.

The KRHRP monitoring and adaptive management plan is guided by the four KRHRP goals (i.e., restore physical habitat by reducing the negative effects to river and floodplain ecological processes caused by river response to the altered landscape; restore native vegetation by establishing stream bank and floodplain conditions that sustain plant community development processes; restore aquatic habitat conditions that support sustainable populations for all life stages of native fish; and create opportunities for river and floodplain stewardship in the community).  Because the KRHRP focuses on addressing limiting factors related to habitat conditions, the KRHRP monitoring and adaptive management plan emphasizes collection and evaluation of data that determines whether habitat goals and objectives are being achieved.  The metrics associated with the KRHRP monitoring and adaptive management plan are designed to measure physical response to habitat restoration treatments implemented as part of the KRHRP.  The Tribe has not established an independent biological monitoring program because biological metrics are being monitored as part of other, concurrent monitoring and evaluation programs, (i.e., Idaho Department of Fish and Game project 198806500, Kootenai Tribe project 199404900 and additional complementary efforts by the British Columbia Ministry of Forests Land Natural Resources Operations and Montana Fish Wildlife and Parks).  Progress towards meeting biological objectives will be evaluated in the context of the annual KRHRP adaptive management plan work session with the Core Adaptive Management Team, as well as in coordination with the Kootenai River White Sturgeon Recovery Team and Burbot Conservation Subcommittee and other mechanisms.  Once completed, the Tribe’s subbasin-scale adaptive management plan will also provide another mechanism to look at short- and long-term trends relative to different metrics including biological responses.

Quantitative habitat objectives are developed for each individual project within the KRHRP (success criteria) and for the KRHRP as a whole.  An example of the incremental quantitative habitat objectives identified for the Phase 1, 1a and 1b projects in the Braided Reach is presented in Table 3.  KRHRP success criteria are presented in the KRHRP adaptive management plan (see subsequent response to ISRP request). 

Table 3. Short-term and long-term success criteria for KRHRP Phase 1a and 1b projects relative to each KRHRP project goal.

Metrics

Short-term success criteria

(0-15 years)

Long-term success criteria

(15+ years)

Morphology

Groundwater depth

 

Groundwater depth corresponds to mainstem flow levels

Floodplain supports vegetation cover types CS, RS or CF

Canopy cover of plants

Shows trend toward CS, RS or CF cover types

CS, RS or CF cover types are present in desired proportional distributions

Area and stability of depositional surfaces

80% or greater of depositional surfaces correspond to ecologically significant flows (between elevations 1771 and 1773 for Phase 1a and between elevations 1764 and 1767 for Phase 1b)

Surfaces are able to support design plant communities

LWD Counts

Number of pieces of LWD is at least 80% of as-built quantity

Vegetated surfaces contribute LWD to the system

Bank erosion rates

Average bank erosion rates are less than 0.1 ft per year

Average bank erosion rates are less than 0.1 ft per year

Hydrologic connectivity

 

80% of modeled water surface elevations for ecologically significant flows (16,000cfs to 24,000 cfs) are between elevations 1771 and 1773 for Phase 1a and between 1764 and 1767 for Phase 1b

Constructed floodplain surfaces support desired distribution of plant communities

Side channel flow capacity

Right side channel conveys 5 to 10% of total flow in the mainstem

Right channel conveys 5 to 10% of total flow in the mainstem

Left side channel is active at flows greater than 20,000 cfs

Left side channel accretes and develops into a floodplain surface

Floodplain Substrate

60% of floodplain surfaces contain sand and/or silt

Constructed floodplain surfaces support desired distribution of plant communities

Structures

Structures control bank stability

Structures decompose

Riparian vegetation

Seedling Density

Seeded species 20/sq ft yrs 1 and 2

Ground surface has veg/litter cover appropriate for the cover type

Canopy cover

Within range for cover type

Within range for cover type

Hydrologic Connectivity

Primary surface hydrology indicators used for wetland delineations are present

Cover types are developing in expected proportions and hydrology indicators continue to be present

Survival

80% of woody containerized plants

N/A

Density

Optional metric—calculate from data if needed

N/A

Weeds

< 10% cover of noxious weeds

Cover types are within ranges

Aquatic habitat

Hydraulic complexity (side channel geometry)

Side channel geometry is within 20% of design criteria

Side channel geometry is within 30% of design criteria

Species population / Proportional distribution

See lower trophic level discussion below

See lower trophic level discussion below

Overhanging bank vegetation

Mature shrubs overhang > 60% of outer banks in side channel by year 10

Mature shrubs overhang > 80% of banks in side channel

Channel Particle size distribution

60-80% gravel/cobble bed

60-80% gravel/cobble bed

Pool/riffle habitat length

30-40% Pool

60-70% Riffle

30-40% Pool

60-70% Riffle

Pool Spacing

Pool spacing = 5 to 7 bankfull widths

Pool spacing = 5 to 7 bankfull widths

Bank Canopy Cover

30 to 50% cover as measured by bioengineering monitoring protocol in Appendix D

>50% cover as measured by densitometer 3 ft from bank, 1 ft above water surface

Integrity and observed function of LWD structures in right side channel

Pool habitat is maintained by structures

 

Pool spacing = 5 to 7 bankfull widths

Pool habitat is maintained by natural processes such as LWD recruitment and lateral scour from meander migration.

River stewardship

Forage utilization

No livestock use of vegetation within exclosure

No reduction in woody vegetation cover due to livestock use

Woody vegetation browse

< 20% utilization of woody plants by wildlife

Wildlife browse not limiting vegetation establishment

Observed livestock use (ex. Hoof prints, trails)

No livestock use within exclosure

Livestock use not causing bank erosion

Landowner agreement in place and in compliance

Confirm yes/no

In compliance

2.  Initial identification and review of Phase 2 and Phase 3 design concepts

The Master Plan was developed in coordination with the Tribe’s Co-manager Agency Review Team (CMART) and Peer Reviewer Advisory Team (PRAT).  The design concepts for Phase 2 and 3 projects were identified using the Master Plan framework as a guide, and refined through a combination of field observations, modeling, spatial analysis, and formal workshops with the CMART and PRAT (see response to ISRP comment number 5 for additional details on these groups).   

After completion of the Master Plan, in order to refine the design concepts for initial consideration, the Tribe’s design team conducted an extended field evaluation to systematically observe how limiting factors are affecting different locations within the Braided and Straight Reaches, which encompass the Phase 2 area.  This resulted in splitting the Straight Reach and Braided Reaches into four distinct segments for internal analysis purposes, based on how the Kootenai River and floodplain is responding to energy movement and system wide stressors such as infrastructure.  The upstream portion has a higher gradient, lacks complex in-channel features such as log jams, has sparse riparian vegetation and limited connected floodplain surfaces, and lacks bank vegetation.  These conditions result in frequent scour of floodplain surfaces and rapid bank erosion.  Side channels are present, but a defined main channel is also present.  The next downstream segment is similar to the furthest upstream reach because there is a main channel that is not over-widened, and some side channels and islands are present.  The gradient is lower through this segment, and the Kootenay Lake backwater affects sediment transport and deposition in the lower portion.  Significant bank erosion is also occurring in this second segment.  The third downstream segment is greatly over-widened, resulting in a braided main channel where islands have either formed, or exist as remnants of previous floodplain surfaces.  The furthest downstream segment is the Straight Reach through Bonners Ferry.  This segment is confined by levees, and lacks complex in-channel habitat. 

Once these distinct segments were identified within Phase 2, the design team completed hydraulic modeling, compared field-collected vegetation data to LiDAR surfaces and flood inundation models, plotted longitudinal profiles, and compiled other data related to limiting factors such as pool frequency and bank erosion.  As part of the development of the Phase 2 design concepts, design team members also visited, with one of the PRAT members, a reference site on the lower Columbia River where habitat is present that supports multiple life stages of white sturgeon.

This information and support analysis was then refined and an initial set of Phase 2 design concepts (10% design) presented to the PRAT as part of a two-day workshop in Bonners Ferry in June 2010.  This workshop also included a tour of the project area so that all the PRAT members would have working understanding of the actual physical characteristics of the project reaches.  As a result of this workshop the initial Phase 2 design concepts were refined and some new concepts added.  In September 2010 the Tribe hosted a second workshop with the CMART members to review the revised Phase 2 design concepts.  One of the outcomes from these workshops was the confirmation of a suite of projects designed to work together within specific areas of a river reach, and specifically discussion of a “pool ladder concept” which involves development and enhancement of a series of pools in the Braided Reach and discussions regarding habitat-based approaches to enhancing food web support in the Kootenai River.  

The Tribe’s design team worked through the fall and early winter of 2011 to refine a suite of project elements that would continue to fit within the Master Plan framework, and address as complete a set of limiting factors as possible, while also identifying opportunities to develop nodes of primary production through the Phase 2 project area and incorporate the ladder concept.  Continued site-specific analyses and input from biologists gained through the collaborative multidisciplinary design process resulted in combining the project elements into a discrete set of projects that can be completed sequentially over several consecutive construction seasons.  These projects in the Braided Reaches and Straight Reach are designed to compliment each other and when implemented as a group will address the restoration strategies identified for each reach.

In February 2011, the Tribe presented an updated suite of Phase 2 design concepts at a joint PRAT and CMART workshop in Spokane, WA.  Information presented included a summary of the specific limiting factors addressed by each concept design, and illustration of the design concept, the desired outcome, and an initial identification of critical feasibility questions that needed to be addressed.  The PRAT and CMART members were asked to provide specific input on design criteria related to focal species habitat requirements, identify the strengths and weaknesses of the concept design from the perspective of their ability to address limiting factors associated with the focal fish species, in terms of proposed design components, location, and effectiveness relationship or in combination with other projects.  The co-managers and Peer Review team also ranked the projects in order of implementation priority and this ranking helped support development of a draft schedule identifying the order in which projects would be completed (some of the other considerations in scheduling include design complexity, permitting complexity, funding, and adaptive management benefits associated with implementing some projects prior to others).  These same design concepts were discussed again with co-managers and technical advisors at a meeting on Braided Reach ecosystem restoration alternatives hosted by the Tribe and U.S. Army Corps of Engineers in March 2011.  In September and October of 2011 the Tribe met with all of the potential Phase 2 project affected landowners to present the initial design concepts to them and ask if they would be willing in concept to see the designs implemented.  This is obviously a critical feasibility question (one of many others) and without this initial acceptance from the landowners the design concepts would not move forward at all.  All of the landowners agreed to continue forward with the design process and were supportive of the initial concepts. 

Figure 1 provides an illustration of a recent analysis of existing versus proposed pool habitat and shows the additional pools that would be created through the combined implementation of a number of the individual KRHRP Phase 2 projects. 

image002

Figure 1. Illustration of existing and proposed pool habitat in Kootenai River Braided Reach 1, Braided Reach 2 and Straight Reach. 

The Phase 2 design concepts presented in the November 2011 proposal are the result of this planning and review process, and represent the collaborative efforts of a large number of knowledgeable individuals with a great deal of expertise including expertise in restoration implementation in general, and specific knowledge regarding the Kootenai River system. 

As described in the proposal, the project team has begun to identify potential Phase 3 projects, and these have also been identified using criteria from the Master Plan.  Within the Meander Reach floodplain, opportunities for restoration are defined in terms of ecological potential for wetland and riparian habitat restoration as determined by elevation, past presence of wetlands, existing vegetation cover, and presence of hydric soils.  The suitability analysis used to identify initial priorities and opportunities for Phase 3 projects is included in Section 4 of the Master Plan, and is also highlighted as a restoration ecology planning case study in Howell et. al. (2011).  Based on these criteria, several projects were selected as potential Phase 3 projects.  The selection and design of Phase 3 projects will follow the same process outlined above and will benefit from the knowledge gained during the design, implementation, and effectiveness monitoring associated with completed Phase 1 and Phase 2 projects.  Additionally, uncertainties research regarding early life stage habitat use of white sturgeon proposed by this project may provide critical information to be incorporated into the design criteria for Phase 3 projects.  The Tribe’s Reconnect project (200200800) also is working to reconnect the historical floodplain and the Kootenai River in the Meander Reaches.  The KRHRP design team is coordinating with the Tribe’s Reconnect project team to share data, analysis and design information in support of restoration efforts in the Meander Reaches.

3.  Summary of design stages and related activities.

Table 4 provides an overview of the types of activities associated with each stage of the design process and the approximate design and implementation schedule for a typical Phase 2 project over an 18-month cycle.  This table is not inclusive of all activities associated with each design stage.  Nor does it incorporate monitoring activities, which would extend well beyond the construction implementation time frame.  The project timeline example in Table 4 assumes that environmental compliance requirements could be met with a BA, an EA or EIS would in most cases add and additional 12 months to the timeline. 

A couple critical points associated with implementation of habitat restoration in the Kootenai River subbasin are important to note.  The first is that the majority of land in the Kootenai Valley is privately owned; therefore, willing and satisfied landowners are critical to the short- and long-term success of the KRHRP and the Tribe’s relationships in the community.  The Tribe coordinates intensely with individual landowners during design and implementation, often speaking one-on-one with landowners during the final design and implementation stages as often as once or twice a week or more, if necessary, to be sure that they are on board with the project, not just in concept, but in reality.  For example, construction staging areas and activities can interfere with grazing areas so landowners with livestock need to make arrangements for an alternate location for their livestock well ahead of construction, some landowners have a higher tolerance for materials staging space and duration than others (i.e., some don’t want to look at a pile of rocks and hundreds of root-wad trees all summer so material acquisition needs to coordinated and timed appropriately), coordination for the use of single lane access roads to accommodate landowner and construction traffic use, and landowner satisfaction with the finished project are several examples of the importance of frequent coordination.

A second critical issue is that the in-water work window in the Kootenai River is only three months long (September – November), so timing of design, review and permitting is has to be very carefully orchestrated.  A delay at any stage of the project can easily push implementation of a project out a year beyond schedule. 

Table 4.  Example of feasibility analysis, design and implementation activities for average KRHRP project requiring BA; for projects requiring an EA or EIS schedule would extend another 12 +/- months. 

image002

In addition to the activities identified in Table 4 above, monitoring for each project would occur throughout much of the year and would include field data collection, data processing and reporting, review and interpretation of results (including adaptive management), and maintenance. 

Table 5 projects a summary of the key technical components associated with each stage of the design process.

Table 5.  Summary of design level, design platform, technical task and level of detail and submittal purpose(s).

Design Level

Design Platform

Technical Task and Level of Detail

Submittal Purpose(s)

Conceptual Design Figures/3D renderings (10%)

GIS

  • Identify project extents based on presence of limiting factors
  • Identify structure types based on restoration strategies
  • Identify structure locations based on initial field review
  • Identify access roads and staging areas
  • Prepare 10% conceptual cost estimate

Support Environmental Assessment and public planning process (including landowner outreach)

Draft Preliminary Design Drawings (35%)

CAD

  • Conduct topographic surveys and develop existing ground surfaces
  • Inventory utilities and site infrastructure
  • Field review design concepts for refinement of project extents
  • Synthesize geomorphic, ecologic, and biological design criteria
  • Develop alignments for proposed channels and banklines
  • Prepare existing conditions HEC-RAS (one-dimensional) hydraulic model to support engineering calculations
  • Prepare preliminary structure details
  • Develop resource protection plans including work area isolation and dewatering plans
  • Prepare 35% preliminary cost estimate

Support Biological Assessment and Feasibility Report

 

 

Preliminary Design Drawings (60%)

CAD

  • Develop grading plans for finished ground surfaces
  • Refine structure details
  • Finalize resource protection plans
  • Prepare proposed conditions HEC-RAS (one-dimensional) hydraulic model to support analysis of project effects
  • Process hydraulic model output (depth and velocity) to support aquatic habitat analysis
  • Prepare preliminary revegetation designs

Support 404 JPA and other permit submittals.

 

Provide technical information for constructability reviews and peer reviews

Final Design Drawings (100%)

CAD

  • Refine finished ground surfaces and structure details based on review engineering calculations and habitat analysis
  • Refine revegetation plans
  • Incorporate final drawing edits from internal and peer QA/QC reviews
  • Update models and confirm project effects
  • Prepare specifications for bid package
  • Prepare engineers cost estimate

Support bid package/contract development and construction

 Planning Framework and Context

In order to conduct feasibility analysis, design development, planning and coordination for the KRHRP the Tribe has assembled a project management team that includes: the core project design team (river design engineers, civil engineers, hydraulic modeling,  riparian restoration, etc.), environmental compliance and permitting experts, cost estimation and contracting expertise, communications and outreach expertise, legal expertise, and project management expertise.  This project management team meets by phone bi-weekly throughout the year to coordinate development of feasibility analysis, design, review processes and workshops, contracting, outreach and communications, and address critical issues associated with every planning and design phase and implementation.  The project management team also meets twice a year for extended planning and coordination sessions.  Additional coordination teams and mechanisms are described in the original project proposal and in our response to the ISRP’s question 5.

To help provide an understanding of the level of outreach and coordination associated with analysis, design and implementation of each project.  Here is a partial list of the agencies and organizations that were involved in some aspect of the analysis, design and implementation of the Phase 1a and 1b KRHRP projects:

  • BC Ministry of Forests Land and Natural Resource Operations (BC MFLRNRO)
  • Bureau of Land Management (BLM)
  • Bonneville Power Administration (BPA)
  • Boundary County
  • City of Bonners Ferry
  • Co-manager and Agency Review Team (CMART)
  • Confederated Salish and Kootenai Tribes (CSKT)
  • Idaho Department of Fish and Game (IDFG)
  • Idaho Department of Lands (IDL)
  • Idaho Department of Environmental Quality (IDEQ)
  • Idaho Department of Water Resources (IDWR)
  • Idaho Office of Species Conservation (OSC)
  • Kootenai Tribal Council
  • Kootenai Valley Resource Initiative (KVRI)
  • Montana Fish Wildlife and Parks (MFWP)
  • Natural Resource Conservation Service (NRCS)
  • Northwest Power and Conservation Council (NPCC)
  • Phase 1 Landowners
  • Peer Review Advisory Team (PRAT)
  • U.S. Army Corp of Engineers (USACE)
  • U.S. Fish and Wildlife Service (USFWS)
  • U.S. Forest Service (USFS)
  • U.S. Geological Survey (USGS)

Additional detail relative to each design stage is provided in the subsequent discussion.

Concept Level Design (10%)

The concept design stage includes development of 10% design concepts and 3D renderings.  The purposes of these concept level designs include:

  • Identifying project extents in relationship to limiting factors
  • Identifying appropriate structure types to use in the designs based on restoration strategies associated with the reach and projects
  • Identifying structure locations based on initial field review
  • Illustrating the relationship of combinations of project concepts at a reach scale
  • Identifying access roads and staging areas
  • Communicating with landowners, agencies, technical reviewers and other stakeholders
  • Identifying initial feasibility issues associated with the project
  • Confirming landowner willingness to move forward with design process
  • Supporting environmental assessment and public planning processes

At this stage of the process the Tribe conducts initial outreach to landowners, project technical team members, agencies and other key stakeholders to explore the feasibility of moving beyond the concept design and to seek approval for the initial design concepts.  All of the Phase 2 designs have been vetted through the concept level design process described previously.  The Tribe also hosted public meetings for the general community in 2011 to present the Phase 2 design concepts and update the community on the Phase 1 project progress.  

Preliminary Design Stage (35% to 60%)

The draft preliminary design (or preliminary design stage 1) includes development of a 35% design.  The activities conducted in the 35% preliminary design stage and purposes of this design stage include:

  • Conducting topographic surveys and developing existing ground surfaces
  • Conducting an inventory of utilities and site infrastructure
  • Completing a field review of design concepts for refinement of project extents
  • Synthesizing geomorphic, ecologic, and biological design criteria
  • Developing alignments for proposed channels and banklines
  • Preparing an existing conditions HEC-RAS (one-dimensional) hydraulic model to support engineering calculations
  • Preparing preliminary structure details
  • Developing resource protection plans including work area isolation and dewatering plans
  • Confirming environmental compliance and permitting requirements
  • Developing supporting information for BA development and initiation of other permitting efforts
  • Supporting landowner, agency, and community outreach (e.g., KVRI)
  • Securing landowner input on preliminary design development (e.g., specific concerns regarding design components, placement of staging areas and access roads, special considerations relative to landowner property or livestock management, etc.)
  • Coordination with Natural Resources Conservation Service (NRCS) on Cooperative Conservation Partnership Initiative (see original proposal for discussion of the CCPI grant the Tribe developed to compliment the KRHRP) landowner participants and design of fencing, seeding and other complimentary actions.
  • Initiate flow request for construction season

The primary purpose of the 35% design is to generate sufficient information to confirm environmental compliance and permitting requirements and initiate development of the BA or EA or EIS.  This stage also helps to identify uncertainties related to design criteria, structures, etc. so that additional data or information can be gathered to support the 60% design via outreach to agencies, landowners, and one-on-one coordination with PRAT and/or CMART members and other experts.  Work on development of a feasibility analysis and preliminary design document for each project is initiated at this stage and culminates with the 60% design.

Preliminary design stage 2 includes development of a 60% design.  The activities conducted in the 60% preliminary design stage and purposes of this design stage include:

  • Develop grading plans for finished ground surfaces
  • Refine structure details
  • Finalizing resource protection plans
  • Preparing proposed conditions HEC-RAS (one-dimensional) hydraulic model to support analysis of project effects
  • Processing hydraulic model output (depth and velocity) to support aquatic habitat analysis
  • Preparing preliminary revegetation designs
  • Completion of a feasibility analysis and preliminary design document
  • Distribution of the feasibility analysis and preliminary design document to PRAT and CMART members for review
  • Completion of a constructability review (this is QA/QC by qualified contractor)
  • Development of sufficient project detail to inform KRHRP policy team briefings (e.g., 60% designs, cost estimates, schedule, identification of any policy issues, etc.)
  • Ensure that flow request for the in-water construction period is submitted and evaluated in the FCRPS System Operation Review (SOR) process and respond to informational requests
  • Development and initiation of materials acquisition plans
  • Development of specific language for inclusion in landowner and access agreements associated with the project
  • Development and completion of signed landowner and access agreements (includes on-on-one meeting with all landowners to review preliminary design and specific staging, access, construction and other activities)
  • Completing and submittal of a BA (if a EA or EIS is developed scoping efforts would be initiated at the 10% design and refined at 35% design and information for the EA or EIS developed at this stage)
  • Developing materials to support the 404 Joint Permit Application and other permit submittals
  • Conducting KVRI briefings and community outreach

The completion of the 60% design provides critical support for the environmental compliance processes and constructability reviews.  Examples of additional critical coordination at this stage include development and completion of landowner and access agreements, outreach and coordination with county and state agencies, and identification of sources of construction materials.  The Tribe also produces a feasibility analysis and preliminary design document at this stage, which is distributed to the CMART and PRAT members for review.  This feasibility analysis and preliminary design document includes the following information:

  • An overview of existing conditions in the project area;
  • Proposed conditions;
  • Relationship of the individual project to other planned or implemented KRHRP projects;
  • Feasibility and design considerations including: analysis of technical risk and uncertainty, aquatic focal species, ecosystem and food web, landowner and land management issues, social and community issues and implementation considerations;
  • A detailed description of the proposed preliminary design for the project including a description of how the project will be implemented, structural components, planting designs, work area isolation plans, BMPs, etc.;
  • A summary of regulatory requirements and the status of compliance at the time the feasibility assessment and preliminary design was completed;
  • An overview of the monitoring program components (the monitoring plan is completed at the final design stage);
  • A summary of the proposed short- and long-term success criteria for the project (restoration indicators); and
  • 60% design drawings. 

There is a substantial amount of analysis and design information presented in these feasibility analysis and design documents that helps to illustrate the work associated with this project design stage and previous stages.  The draft Feasibility Analysis and Preliminary Design Document for the Phase 2, Upper Meander and North Side Channels projects (scheduled for implementation in 2012) is posted at: http://www.restoringthekootenai.org/ResourcesKootenai/OnlineLibrary/isrpreviewlibrary/ 

Input from the PRAT and CMART review of the feasibility analysis and preliminary designs is incorporated into the final design stage and also used to help compile enhanced biological and design information for use in development of future KRHRP projects.  If any critical issues are raised during the review that haven’t somehow been identified in previous workshops or in one-on-one outreach to the PRAT and CMART members, additional workshops or smaller working meetings can be scheduled to address those issues.  An example of this is the proposed 1135 substrate augmentation project where concerns were raised in the co-manager and agency review of the feasibility design, that are currently being investigated through a technical modeling workshop and additional targeted feasibility analysis.  Pending the outcome of this additional work a follow-up workshop with the entire technical advisory group may be convened to discuss modifications to the preliminary design (more information on this is provided later in this response as part of a response to specific ISRP questions on the 1135 project). 

The sequential iterative development, review, implementation and monitoring of each KRHRP project (as opposed to designing all of the projects at once) is a critical component of the KRHRP approach.  As each project comes on line for design and implementation, a better suite of information is available to support design and implementation. 

Final design and contracting stage (90% to 100%)

The final design stage includes development of a 90% and 100% design.  The activities conducted in the final design stage and purposes of this design stage include:

  • Refining the finished ground surfaces and structure details based on review engineering calculations and habitat analysis
  • Refining revegetation plans
  • Incorporating final drawing edits from internal and peer QA/QC reviews
  • Updating models and confirming project effects
  • Preparing specifications for the construction bid package
  • Preparing engineer’s cost estimate
  • Bid solicitation and selection of construction contractor(s)
  • Development and completion of construction contract
  • Continued materials acquisition work
  • Completion of all required permitting
  • Coordination with utilities and infrastructure owners to ensure all permits, agreements and contacts are in place (e.g., railroad permitting requirements, etc.)
  • Confirm construction flow arrangements and timing
  • Development of final monitoring and evaluation plan for project (includes coordination with IDFG, other Tribal projects, and BC MLFNRO)
  • Final coordination with affected landowners, county and state agencies, and Federal agencies if relevant to project location
  • Public meetings to inform the public regarding the season’s construction work and details.

The primary purposes of the final design stage is to complete all design, permitting and coordination planning necessary to successfully implement the project.

Implementation stage

Planning and coordination don’t end with feasibility analysis and design work.  The implementation stage includes the following activities:  

  • Completion of pre-construction monitoring and documentation
  • Mobilization of equipment and development of construction infrastructure
  • Development of access routes and materials staging areas
  • Acquisition and staging of construction materials (depending on the final scope of the specific project, some materials acquisition and staging may occur over one or more years)
  • Site preparation
  • Implementation of construction activities during approved construction work window (construction implementation may occur over one or more years depending on the specifics of the individual project)
  • Complete planting, seeding and fencing
  • Coordination with NRCS on implementation of CCPI activities
  • Implementation of post construction reclamation activities
  • Demobilization of equipment and associated construction infrastructure
  • Completion of as-build monitoring
  • Project completion debrief work session
  • Conduct scheduled project tours and site visits as requested by various parties
  • Daily construction meetings
  • Ongoing (generally daily or weekly) coordination with landowners
  • Community briefings to county and state agencies, KVRI

During the project implementation stage the Tribe’s project manager, general contractor, and design engineer coordinate frequently, sometime even daily.  The Tribe and the general contractor also coordinate on a frequent basis with affected landowners.  Daily construction reports are developed and posted on the Tribe’s internal web site.  Ongoing coordination with regulatory agencies, county government and other entities occurs throughout the implementation process.  Other activities that aren’t necessarily formally reflected are the overall coordination that occurs throughout the implementation process.  During the 2011 construction season, a team of biologists and volunteers from IDFG, BCMFLNRO, the Kootenai Tribe, USACE and the community participated in the fish rescue activities associated with the project dewatering work.

At the end of the construction season, after demobilization work has been completed the Tribe also convenes a project debriefing session with the entire design, planning and implementation team.  The purpose of this session is review every aspect of planning, feasibility assessment, design, outreach, review, contracting, implementation and general coordination to identify lessons learned (i.e., what worked well, what didn’t, what surprises occurred) and identify mechanisms to better address those issues in future projects and to plan the subsequent season’s design and construction schedule.  The Tribe convened a three-day session in December 2011 to review every aspect of the Phase 1a and 1b projects and to develop a detailed schedule with deliverables and milestones for the 2012-2013 construction season.  

RME and adaptive management

As previously described, the Tribe is developing a monitoring and evaluation plan for each individual KRHRP project during the preliminary and final design stages.  Each monitoring and evaluation plan will include the following components:

  • Summary of limiting factors, objectives and metrics associated with the project
  • Monitoring program components including baseline monitoring, construction and as-built monitoring and effectiveness monitoring
  • Monitoring schedule
  • Restoration indicators
  • An overview of the adaptive management decision-making framework
  • Appendix with monitoring methods
  • Appendix with cover type descriptions

The overarching adaptive management plan for the KRHRP is the KRHRP monitoring and adaptive management plan.  The KRHRP monitoring and adaptive management plan will be implemented through annual meetings with the Core Adaptive Management Team in the fall of each year.  The Core Adaptive Management Team includes representatives from the Kootenai Tribe, IDFG, BCNFLNRO, and MFWP as well as additional expertise as necessary to assist in review and interpretation of the monitoring results.  Additional description and the working draft KRHRP Adaptive Management Plan is provided with this response to the ISRP. 

Research conducted as part of this project (i.e., Kootenai River side-channel research, early life stage research) and through other efforts in the Kootenai subbasin or relevant specifically to white sturgeon or other focal species populations will be incorporated into development of the design criteria for each project as it is developed and reviewed.  In addition, we will discuss the results of research findings and additional research needs in the context of adaptively managing implementation of the KRHRP at the following venues: Core Adaptive Management Team annual meetings, Kootenai River White Sturgeon Recovery Team meetings, Burbot Conservation Subcommittee meetings, and other technical coordination groups associated with the Tribe’s programs (see discussion of project integration in response to ISRP comment 5 for additional detail).

Monitoring information gathered through implementation of the KRHRP each year will be critical to helping refine the designs for KRHRP projects scheduled for implementation in subsequent years.  For example, the Upper Meander project slated for construction in 2012 includes design structures that are proposed for use in projects to be implemented in subsequent years.  Information derived from monitoring of the Upper Meander project will provide valuable input to evaluate the physical characteristics of:

  • Stability of timber piles
  • Stability of backfill within pile fields and structure interior
  • Changes in pool characteristics (depth, velocity, substrate, scour, deposition)
  • Changes in eddy characteristics (depth, velocity, substrate, scour, deposition)
  • Effects on adjacent banks and reaches
  • Effectiveness and efficiency of construction means and methods

This information will then be used to refine the structural design and placement of specific structures in future KRHRP projects (e.g., the Straight Reach and Bonners Ferry Island projects). 

In addition, the most recent biological information collected through the IDFG sturgeon and burbot monitoring program, the Tribal/IDFG biomonitoring program (project 199404900), and other monitoring efforts (e.g., side channel), will evaluated as part of the development of design criteria for each KRHRP project as it is designed.  The opportunity to continuously incorporate the most up to date technical monitoring data, biological monitoring data and research findings into the individual project designs for the KRHRP is a major reason that the Tribe feels so strongly that the iterative design and review process we’ve developed to implement the KRHRP is the most efficient, precautionary, and defensible approach to implementation of this large-scale KRHRP.  

Planning Framework and Context

In order to conduct feasibility analysis, design development, planning and coordination for the KRHRP the Tribe has assembled a project management team that includes: the core project design team (river design engineers, civil engineers, hydraulic modeling,  riparian restoration, etc.), environmental compliance and permitting experts, cost estimation and contracting expertise, communications and outreach expertise, legal expertise, and project management expertise.  This project management team meets by phone bi-weekly throughout the year to coordinate development of feasibility analysis, design, review processes and workshops, contracting, outreach and communications, and address critical issues associated with every planning and design phase and implementation.  The project management team also meets twice a year for extended planning and coordination sessions.  Additional coordination teams and mechanisms are described in the original project proposal and in our response to the ISRP’s question 5.

To help provide an understanding of the level of outreach and coordination associated with analysis, design and implementation of each project.  Here is a partial list of the agencies and organizations that were involved in some aspect of the analysis, design and implementation of the Phase 1a and 1b KRHRP projects:

  • BC Ministry of Forests Land and Natural Resource Operations (BC MFLRNRO)
  • Bureau of Land Management (BLM)
  • Bonneville Power Administration (BPA)
  • Boundary County
  • City of Bonners Ferry
  • Co-manager and Agency Review Team (CMART)
  • Confederated Salish and Kootenai Tribes (CSKT)
  • Idaho Department of Fish and Game (IDFG)
  • Idaho Department of Lands (IDL)
  • Idaho Department of Environmental Quality (IDEQ)
  • Idaho Department of Water Resources (IDWR)
  • Idaho Office of Species Conservation (OSC)
  • Kootenai Tribal Council
  • Kootenai Valley Resource Initiative (KVRI)
  • Montana Fish Wildlife and Parks (MFWP)
  • Natural Resource Conservation Service (NRCS)
  • Northwest Power and Conservation Council (NPCC)
  • Phase 1 Landowners
  • Peer Review Advisory Team (PRAT)
  • U.S. Army Corp of Engineers (USACE)
  • U.S. Fish and Wildlife Service (USFWS)
  • U.S. Forest Service (USFS)
  • U.S. Geological Survey (USGS)

Additional detail relative to each design stage is provided in the subsequent discussion.

Concept Level Design (10%)

The concept design stage includes development of 10% design concepts and 3D renderings.  The purposes of these concept level designs include:

  • Identifying project extents in relationship to limiting factors
  • Identifying appropriate structure types to use in the designs based on restoration strategies associated with the reach and projects
  • Identifying structure locations based on initial field review
  • Illustrating the relationship of combinations of project concepts at a reach scale
  • Identifying access roads and staging areas
  • Communicating with landowners, agencies, technical reviewers and other stakeholders
  • Identifying initial feasibility issues associated with the project
  • Confirming landowner willingness to move forward with design process
  • Supporting environmental assessment and public planning processes

At this stage of the process the Tribe conducts initial outreach to landowners, project technical team members, agencies and other key stakeholders to explore the feasibility of moving beyond the concept design and to seek approval for the initial design concepts.  All of the Phase 2 designs have been vetted through the concept level design process described previously.  The Tribe also hosted public meetings for the general community in 2011 to present the Phase 2 design concepts and update the community on the Phase 1 project progress.  

Preliminary Design Stage (35% to 60%)

The draft preliminary design (or preliminary design stage 1) includes development of a 35% design.  The activities conducted in the 35% preliminary design stage and purposes of this design stage include:

  • Conducting topographic surveys and developing existing ground surfaces
  • Conducting an inventory of utilities and site infrastructure
  • Completing a field review of design concepts for refinement of project extents
  • Synthesizing geomorphic, ecologic, and biological design criteria
  • Developing alignments for proposed channels and banklines
  • Preparing an existing conditions HEC-RAS (one-dimensional) hydraulic model to support engineering calculations
  • Preparing preliminary structure details
  • Developing resource protection plans including work area isolation and dewatering plans
  • Confirming environmental compliance and permitting requirements
  • Developing supporting information for BA development and initiation of other permitting efforts
  • Supporting landowner, agency, and community outreach (e.g., KVRI)
  • Securing landowner input on preliminary design development (e.g., specific concerns regarding design components, placement of staging areas and access roads, special considerations relative to landowner property or livestock management, etc.)
  • Coordination with Natural Resources Conservation Service (NRCS) on Cooperative Conservation Partnership Initiative (see original proposal for discussion of the CCPI grant the Tribe developed to compliment the KRHRP) landowner participants and design of fencing, seeding and other complimentary actions.
  • Initiate flow request for construction season

The primary purpose of the 35% design is to generate sufficient information to confirm environmental compliance and permitting requirements and initiate development of the BA or EA or EIS.  This stage also helps to identify uncertainties related to design criteria, structures, etc. so that additional data or information can be gathered to support the 60% design via outreach to agencies, landowners, and one-on-one coordination with PRAT and/or CMART members and other experts.  Work on development of a feasibility analysis and preliminary design document for each project is initiated at this stage and culminates with the 60% design.

Preliminary design stage 2 includes development of a 60% design.  The activities conducted in the 60% preliminary design stage and purposes of this design stage include:

  • Develop grading plans for finished ground surfaces
  • Refine structure details
  • Finalizing resource protection plans
  • Preparing proposed conditions HEC-RAS (one-dimensional) hydraulic model to support analysis of project effects
  • Processing hydraulic model output (depth and velocity) to support aquatic habitat analysis
  • Preparing preliminary revegetation designs
  • Completion of a feasibility analysis and preliminary design document
  • Distribution of the feasibility analysis and preliminary design document to PRAT and CMART members for review
  • Completion of a constructability review (this is QA/QC by qualified contractor)
  • Development of sufficient project detail to inform KRHRP policy team briefings (e.g., 60% designs, cost estimates, schedule, identification of any policy issues, etc.)
  • Ensure that flow request for the in-water construction period is submitted and evaluated in the FCRPS System Operation Review (SOR) process and respond to informational requests
  • Development and initiation of materials acquisition plans
  • Development of specific language for inclusion in landowner and access agreements associated with the project
  • Development and completion of signed landowner and access agreements (includes on-on-one meeting with all landowners to review preliminary design and specific staging, access, construction and other activities)
  • Completing and submittal of a BA (if a EA or EIS is developed scoping efforts would be initiated at the 10% design and refined at 35% design and information for the EA or EIS developed at this stage)
  • Developing materials to support the 404 Joint Permit Application and other permit submittals
  • Conducting KVRI briefings and community outreach

The completion of the 60% design provides critical support for the environmental compliance processes and constructability reviews.  Examples of additional critical coordination at this stage include development and completion of landowner and access agreements, outreach and coordination with county and state agencies, and identification of sources of construction materials.  The Tribe also produces a feasibility analysis and preliminary design document at this stage, which is distributed to the CMART and PRAT members for review.  This feasibility analysis and preliminary design document includes the following information:

  • An overview of existing conditions in the project area;
  • Proposed conditions;
  • Relationship of the individual project to other planned or implemented KRHRP projects;
  • Feasibility and design considerations including: analysis of technical risk and uncertainty, aquatic focal species, ecosystem and food web, landowner and land management issues, social and community issues and implementation considerations;
  • A detailed description of the proposed preliminary design for the project including a description of how the project will be implemented, structural components, planting designs, work area isolation plans, BMPs, etc.;
  • A summary of regulatory requirements and the status of compliance at the time the feasibility assessment and preliminary design was completed;
  • An overview of the monitoring program components (the monitoring plan is completed at the final design stage);
  • A summary of the proposed short- and long-term success criteria for the project (restoration indicators); and
  • 60% design drawings. 

There is a substantial amount of analysis and design information presented in these feasibility analysis and design documents that helps to illustrate the work associated with this project design stage and previous stages.  The draft Feasibility Analysis and Preliminary Design Document for the Phase 2, Upper Meander and North Side Channels projects (scheduled for implementation in 2012) is posted at: http://www.restoringthekootenai.org/ResourcesKootenai/OnlineLibrary/isrpreviewlibrary/ 

Input from the PRAT and CMART review of the feasibility analysis and preliminary designs is incorporated into the final design stage and also used to help compile enhanced biological and design information for use in development of future KRHRP projects.  If any critical issues are raised during the review that haven’t somehow been identified in previous workshops or in one-on-one outreach to the PRAT and CMART members, additional workshops or smaller working meetings can be scheduled to address those issues.  An example of this is the proposed 1135 substrate augmentation project where concerns were raised in the co-manager and agency review of the feasibility design, that are currently being investigated through a technical modeling workshop and additional targeted feasibility analysis.  Pending the outcome of this additional work a follow-up workshop with the entire technical advisory group may be convened to discuss modifications to the preliminary design (more information on this is provided later in this response as part of a response to specific ISRP questions on the 1135 project). 

The sequential iterative development, review, implementation and monitoring of each KRHRP project (as opposed to designing all of the projects at once) is a critical component of the KRHRP approach.  As each project comes on line for design and implementation, a better suite of information is available to support design and implementation. 

Final design and contracting stage (90% to 100%)

The final design stage includes development of a 90% and 100% design.  The activities conducted in the final design stage and purposes of this design stage include:

  • Refining the finished ground surfaces and structure details based on review engineering calculations and habitat analysis
  • Refining revegetation plans
  • Incorporating final drawing edits from internal and peer QA/QC reviews
  • Updating models and confirming project effects
  • Preparing specifications for the construction bid package
  • Preparing engineer’s cost estimate
  • Bid solicitation and selection of construction contractor(s)
  • Development and completion of construction contract
  • Continued materials acquisition work
  • Completion of all required permitting
  • Coordination with utilities and infrastructure owners to ensure all permits, agreements and contacts are in place (e.g., railroad permitting requirements, etc.)
  • Confirm construction flow arrangements and timing
  • Development of final monitoring and evaluation plan for project (includes coordination with IDFG, other Tribal projects, and BC MLFNRO)
  • Final coordination with affected landowners, county and state agencies, and Federal agencies if relevant to project location
  • Public meetings to inform the public regarding the season’s construction work and details.

The primary purposes of the final design stage is to complete all design, permitting and coordination planning necessary to successfully implement the project.

Implementation stage

Planning and coordination don’t end with feasibility analysis and design work.  The implementation stage includes the following activities:  

  • Completion of pre-construction monitoring and documentation
  • Mobilization of equipment and development of construction infrastructure
  • Development of access routes and materials staging areas
  • Acquisition and staging of construction materials (depending on the final scope of the specific project, some materials acquisition and staging may occur over one or more years)
  • Site preparation
  • Implementation of construction activities during approved construction work window (construction implementation may occur over one or more years depending on the specifics of the individual project)
  • Complete planting, seeding and fencing
  • Coordination with NRCS on implementation of CCPI activities
  • Implementation of post construction reclamation activities
  • Demobilization of equipment and associated construction infrastructure
  • Completion of as-build monitoring
  • Project completion debrief work session
  • Conduct scheduled project tours and site visits as requested by various parties
  • Daily construction meetings
  • Ongoing (generally daily or weekly) coordination with landowners
  • Community briefings to county and state agencies, KVRI

During the project implementation stage the Tribe’s project manager, general contractor, and design engineer coordinate frequently, sometime even daily.  The Tribe and the general contractor also coordinate on a frequent basis with affected landowners.  Daily construction reports are developed and posted on the Tribe’s internal web site.  Ongoing coordination with regulatory agencies, county government and other entities occurs throughout the implementation process.  Other activities that aren’t necessarily formally reflected are the overall coordination that occurs throughout the implementation process.  During the 2011 construction season, a team of biologists and volunteers from IDFG, BCMFLNRO, the Kootenai Tribe, USACE and the community participated in the fish rescue activities associated with the project dewatering work.

At the end of the construction season, after demobilization work has been completed the Tribe also convenes a project debriefing session with the entire design, planning and implementation team.  The purpose of this session is review every aspect of planning, feasibility assessment, design, outreach, review, contracting, implementation and general coordination to identify lessons learned (i.e., what worked well, what didn’t, what surprises occurred) and identify mechanisms to better address those issues in future projects and to plan the subsequent season’s design and construction schedule.  The Tribe convened a three-day session in December 2011 to review every aspect of the Phase 1a and 1b projects and to develop a detailed schedule with deliverables and milestones for the 2012-2013 construction season.  

RME and adaptive management

As previously described, the Tribe is developing a monitoring and evaluation plan for each individual KRHRP project during the preliminary and final design stages.  Each monitoring and evaluation plan will include the following components:

  • Summary of limiting factors, objectives and metrics associated with the project
  • Monitoring program components including baseline monitoring, construction and as-built monitoring and effectiveness monitoring
  • Monitoring schedule
  • Restoration indicators
  • An overview of the adaptive management decision-making framework
  • Appendix with monitoring methods
  • Appendix with cover type descriptions

The overarching adaptive management plan for the KRHRP is the KRHRP monitoring and adaptive management plan.  The KRHRP monitoring and adaptive management plan will be implemented through annual meetings with the Core Adaptive Management Team in the fall of each year.  The Core Adaptive Management Team includes representatives from the Kootenai Tribe, IDFG, BCNFLNRO, and MFWP as well as additional expertise as necessary to assist in review and interpretation of the monitoring results.  Additional description and the working draft KRHRP Adaptive Management Plan is provided with this response to the ISRP. 

Research conducted as part of this project (i.e., Kootenai River side-channel research, early life stage research) and through other efforts in the Kootenai subbasin or relevant specifically to white sturgeon or other focal species populations will be incorporated into development of the design criteria for each project as it is developed and reviewed.  In addition, we will discuss the results of research findings and additional research needs in the context of adaptively managing implementation of the KRHRP at the following venues: Core Adaptive Management Team annual meetings, Kootenai River White Sturgeon Recovery Team meetings, Burbot Conservation Subcommittee meetings, and other technical coordination groups associated with the Tribe’s programs (see discussion of project integration in response to ISRP comment 5 for additional detail).

Monitoring information gathered through implementation of the KRHRP each year will be critical to helping refine the designs for KRHRP projects scheduled for implementation in subsequent years.  For example, the Upper Meander project slated for construction in 2012 includes design structures that are proposed for use in projects to be implemented in subsequent years.  Information derived from monitoring of the Upper Meander project will provide valuable input to evaluate the physical characteristics of:

  • Stability of timber piles
  • Stability of backfill within pile fields and structure interior
  • Changes in pool characteristics (depth, velocity, substrate, scour, deposition)
  • Changes in eddy characteristics (depth, velocity, substrate, scour, deposition)
  • Effects on adjacent banks and reaches
  • Effectiveness and efficiency of construction means and methods

This information will then be used to refine the structural design and placement of specific structures in future KRHRP projects (e.g., the Straight Reach and Bonners Ferry Island projects). 

In addition, the most recent biological information collected through the IDFG sturgeon and burbot monitoring program, the Tribal/IDFG biomonitoring program (project 199404900), and other monitoring efforts (e.g., side channel), will evaluated as part of the development of design criteria for each KRHRP project as it is designed.  The opportunity to continuously incorporate the most up to date technical monitoring data, biological monitoring data and research findings into the individual project designs for the KRHRP is a major reason that the Tribe feels so strongly that the iterative design and review process we’ve developed to implement the KRHRP is the most efficient, precautionary, and defensible approach to implementation of this large-scale KRHRP.  

II.  A draft of the KRHRP monitoring and adaptive management plan should be provided.

The ISRP requested a draft of the Kootenai River Habitat Restoration Program (KRHRP) monitoring and adaptive management plan.  The KRHRP monitoring and adaptive management plan framework was provided in Chapter 5 of the Kootenai River Habitat Restoration Project Master Plan.  We have loaded an updated draft of the KRHRP monitoring and adaptive management plan on the project web site at: http://www.restoringthekootenai.org/ResourcesKootenai/OnlineLibrary/isrpreviewlibrary/.

We also wanted to clarify the role and purpose of the various monitoring and evaluation and adaptive management processes that are associated with the Kootenai River Habitat Restoration Program and the Tribe’s other projects, as this may have been confusing in the original proposal.

  • An individual monitoring and evaluation plan for each project within the Kootenai River Habitat Restoration Program will be developed as part of the project design process and will be finalized prior to implementation of the project (i.e., a monitoring and evaluation plan will be developed for the Phase 1a and 1b projects, for the Upper Meander project, for the North Side Channels project, etc.)  By way of example, the Phase 1a and 1b monitoring and evaluation plan is posted at: http://www.restoringthekootenai.org/ResourcesKootenai/OnlineLibrary/isrpreviewlibrary/.
  • The overarching adaptive management plan for the Kootenai River Habitat Restoration Program is the KRHRP monitoring and adaptive management plan.  The KRHRP monitoring and adaptive management plan will be implemented through annual meetings with the Core Adaptive Management Team in the fall of each year.  The Core Adaptive Management Team includes representatives from the Kootenai Tribe, IDFG, BCNFLNRO, and MFWP as well as additional expertise as necessary to assist in review and interpretation of the monitoring results.  Starting from the working draft provided to the ISRP above, the KRHRP monitoring and adaptive management plan will be updated annually by appending each year’s project-specific monitoring plan to the base KRHRP monitoring and adaptive management plan document, and incorporating a summary of the Core Adaptive Management Team deliberations and any related management-decisions. 
  • The Kootenai Tribe’s subbasin-scale adaptive management plan is being developed as a separate effort from the KRHRP monitoring and adaptive management plan.  The purpose of the Kootenai Subbasin Adaptive Management Plan is to link each of the projects within the Tribe’s Fish and Wildlife Program via a subbasin scale framework in order to better understand and adaptively manage how those projects collectively contribute to ecosystem restoration in the Kootenai subbasin.  See additional discussion in response to ISRP question 5, which provides some additional detail regarding the Kootenai Tribe’s subbasin-scale adaptive management plan.

The KRHRP monitoring and adaptive management plan is guided by the four Kootenai River Habitat Restoration Program goals:

  • Restore physical habitat by reducing the negative effects to river and floodplain ecological processes caused by river response to the altered landscape.
  • Restore native vegetation by establishing stream bank and floodplain conditions that sustain plant community development processes.
  • Restore aquatic habitat conditions that support sustainable populations for all life stages of native fish.
  • Create opportunities for river and floodplain stewardship in the community.

The purpose of the KRHRP monitoring and adaptive management plan is to provide a framework to:

  • Evaluate the effectiveness of the implemented habitat actions in terms of achieving the project goals;
  • Identify project maintenance needs;
  • Identify any potential unforeseen negative impacts on infrastructure, public and private lands, flood control management, focal species, and habitat;
  • Support decisions to modify restoration treatments; and
  • Refine or modify restoration treatments that might be implemented in later phases of the project.

Because the Kootenai River Habitat Restoration Program focuses on addressing limiting factors related to habitat conditions, the KRHRP monitoring and adaptive management plan emphasizes collection and evaluation of data that determines whether habitat goals and objectives are being achieved.  The metrics associated with the KRHRP monitoring and adaptive management plan are designed to measure physical response to habitat restoration treatments implemented as part of the Kootenai River Habitat Restoration Program. 

The KRHRP adaptive management and monitoring program does not specifically include metrics related to the biological response of the focal aquatic species populations.  This is largely because those metrics are being monitored as part of other, concurrent monitoring and evaluation programs (i.e., IDFG project 198806500, Kootenai Tribe project 199404900 and additional complementary efforts by the British Columbia Ministry of Forests Land Natural Resources Operations and Montana Fish Wildlife and Parks).  The Tribe has shared access to these data, and data collected through these complementary efforts will be evaluated and reviewed in the context of the KRHRP monitoring and adaptive management plan in the annual Core Adaptive Management Team work sessions.  A table summarizing which biological metrics are being measured by other entities is included in the KRHRP monitoring and adaptive management plan.  Nutrient levels, water quality and biological productivity will all be monitored through the Tribe’s project 199404900 and that data will be considered in the annual Core Adaptive Management Team meeting.  

The ISRP reviewers commented that monitoring of Kootenai sturgeon will need to go on for many decades into the future due to the long life span of sturgeon.  We wholeheartedly agreed.  The physical response monitoring directly associated with this project will have an end point in the relatively near-term, but the Tribe and IDFG will continue to support long-term monitoring of Kootenai sturgeon far into the future.

In addition to the KRHRP monitoring and adaptive management Core Adaptive Management Team work sessions, the relationship of biological response to habitat actions will be reviewed in the context of Kootenai River White Sturgeon Recovery Team meetings, Burbot Conservation Committee work sessions, and the Tribe’s subbasin-scale adaptive management plan once it is completed. 

Winter monitoring activities associated with the Phase 1a and 1b projects are currently underway and the first Core Adaptive Management Team workshop will take place in the fall of 2012. 

 

III.  Ten recruitment failure hypotheses are listed in the proposal.  Identify which of these hypotheses have been tested and what conclusions have been reached.

In our November 2011 proposal we provided a list of ten recruitment failure hypotheses that were developed in 2005.  This information was presented in the context of the regulatory history associated with Kootenai sturgeon and background to the development of the KRHRP Master Plan and the Tribe’s current proposal.  In 2005, the Tribe in coordination with the Recovery Team produced the Kootenai River White Sturgeon Recovery Implementation Plan Schedule for 2005 - 2010 (KTOI 2005).  The Implementation Plan identified research, monitoring and evaluation actions believed necessary to protect, rehabilitate, and maintain Kootenai sturgeon in conjunction with activities highlighted in the population’s Recovery Plan.  Figure 2 summarizes components of the 2005 recovery implementation plan.  

image004

Figure 2. Kootenai River White Sturgeon Recovery Implementation Plan Schedule – 2005-2010 (KTOI 2005).

The 2005-2010 implementation strategy also incorporated a summary of ten current working recruitment failure hypotheses (as of 2005):

  1. Ecosystem degradation
  2. Imprinting/homing failure
  3. Riparian habitat loss
  4. Stock limitation
  5. Flow reduction
  6. Sand invasion
  7. Lack of scour
  8. Upstream migration barrier
  9. Shifted hydraulic cues

10.  Olfactory effect on spawning location

This list of 10 “recruitment failure hypotheses” was generated in 2005 following a series of discussions by the Kootenai River White Sturgeon Recovery Team (RT) that were narrowly focused on flows and Libby Dam operations as the main casual factor for natural recruitment failure.  The list was generated in response to the emerging discussions regarding a broader array of potential alternative or additional limiting factors contributing to recruitment failure.

As of today, none of these “hypotheses” have been formally or statistically tested.  However, fieldwork over the past several decades has provided considerable insight into the degree of relevance for many of the listed hypotheses and improved monitoring designs will help to address some of these questions in the future.  The USFWS recently complete a five-year status review for Kootenai River white sturgeon (Flory 2011) and has recognized the need to update the 1999 Recovery Plan (USFWS 1999).

Updated characterization of recruitment failure hypotheses 

These original (2005) hypotheses were reviewed and discussed at a recent Kootenai River White Sturgeon meeting (3/1/12) as part of discussions about updating the Kootenai sturgeon Recovery Plan.  A summary of these discussions is provided below in the following Table 6.   Each hypothesis is listed, briefly defined, and the critically affected life stage(s) are identified, along with general evidence for and against each hypothesis, the period of influence (pre-and/or post-dam), a mean confidence value assigned by 20 surveyed Recovery Team meeting participants, and a partial list of supporting literature.  To help guide the Recovery Team discussion a 5-point ranking scale was used to determine participant’s relative confidence level for each hypothesis:

Levels of confidence:

  1 = No confidence in hypothesis

  2 = Low level of confidence

  3 = 50/50

  4 = Moderate level of confidence

  5 = High level of confidence

 The Recovery Team meeting participants generally concluded that a suite of additive limiting factors likely contributed to and continues to drive recruitment failure over a period of decades, and that more careful, focused evaluation is needed to tease out the validity and characteristics of each hypotheses.  Participants also agreed that this list of hypotheses and the individual degree of relevance for each originally proposed hypothesis need to be revised and updated as part of the process to update the Kootenai River White Sturgeon Recovery Plan.  

Participants agreed that this group of 2005 “hypotheses” range from collective groupings of potential limiting factors to specific mechanisms suspected of contributing to recruitment failure and need to be broken into sub categories in some cases in order to facilitate additional evaluation.  

Finally, participants also identified the erroneous labeling of some items as exclusively pre- or post-dam factors, noting that some transcend pre- and post-dam time periods.  Modifications to the correct period or periods of effect for each hypothesis are provided (Table 6).  Surveyed Recovery Team meeting participants expressed a wide array of confidence in the recruitment failure hypotheses, ranging from 1.4-4.6 on a scale of 1 to 5 (1=no confidence, 5= strong confidence).  Noted exceptions included H1 and H7, and to a lesser extent H6, H10, and H11 (Figure 3).  Reasons for this divergence included a wide array of beliefs regarding many of the hypotheses, and various interpretations of the hypotheses themselves.

The following Table 6 includes a partial list of literature citations related to each hypothesis.  As part of the process of updating the Recovery Plan, additional focus will be placed on providing a more comprehensive update on these issues and the supporting literature.

Table 6. Characterization of Kootenai River white sturgeon recruitment failure hypotheses.

Hypotheses: 

1. Ecosystem degradation 

Description

Recruitment failure is due to the direct and indirect cascading effects of habitat alteration and loss of the natural floodplain and the flood pulse (e.g., reduced nutrient and food availability, altered competition and predation, and reduced habitat quality and availability).

Critical life stage(s)

Acutely: Spawning, eggs, embryos, free embryos, larvae

Chronically: Juveniles, adults

Supporting evidence

The loss of connectivity and functionality of off-channel and backwater habitats may contribute directly and indirectly to lost recruitment via lost productivity, food availability, and habitat diversity among a naturally diverse mosaic of habitats.  Temporal correlation between natural recruitment failure and completion of continuous lower river levees (~125 km, entire meander reach) separating the main channel from floodplain and off-channel habitat.  Ultimately due to loss of the natural flood pulse and its myriad physical and biological effects in all main channel and off-channel habitats (Junk et al. 1989; Sparks 1994). Recruitment failure appears to have occurred relatively abruptly between 1950 and 1960 and have remained suppressed ever since (Paragamian et al. 2005) rather than gradually over an extended period of time coincident with large scale system changes (e.g. levee completion).

Evidence against

N/A

Period of effects

Pre-dam and Post-dam

Mean confidence value

High (4.6 of 5)

Supporting literature

Anders et al. 2002; Ashley et al. 1999; Northcote 1973; Snyder and Minshall 2005; Junk et al. 1989; Sparks 1994; Paragamian et al. 2005

Hypotheses: 

2. Imprinting/homing failure 

Description

Kootenai sturgeon no longer migrate upstream from Bonners Ferry into what appears to be suitable spawning, incubation, and early rearing habitats in the braided and canyon reaches because fish that historically spawned in these reaches (possibly as far upstream as the “sturgeon hole” at the base of Kootenay Falls) no longer exist.

Critical life stage(s)

Larvae, juveniles, adults  (Assuming sequential imprinting)

Supporting evidence

Anecdotal evidence of spawning as far upstream as sturgeon hole; Kootenai fish have been observed exclusively spawning in the same ~ 18 km reach from Shorty’s Island to the Bonners Ferry area. (A within-population example of site fidelity?).

Strong support for homing to natal areas in most studied sturgeon species.

Empirical post-hatch early life habitat selection experiments (Kynard et al. studies) suggest hatching is occurring up to 2 weeks too far downstream (The observed habitat-early life stage mismatch could be explained by spawning upstream in the canyon or meander reaches).

Evidence against

No distinct and adaptive remnant life history pattern has been observed.  If this life history variant (ecotype) existed, it should have left a signal in the remnant population.

Period of effects

Pre-dam and Post-dam

Mean confidence value

Low (2.3 of 5)

Supporting literature

Kynard et al. (missing specific citations)

Hypotheses: 

3. Riparian habitat loss 

Description

Widespread collapse of resident white sturgeon populations is due primarily to the loss of flooded riparian vegetation, which might provide critical incubation and early rearing conditions

Critical life stage(s)

Larvae, juveniles, adults (all exogenously feeding life stages)

Supporting evidence

Loss of riparian and off-channel habitats temporally correlated with onset and duration of KR WST recruitment failure.

Evidence against

Early life stages from most sampled white sturgeon populations are collected in deep water or thalweg areas of rivers, despite initial disproportionately greater sampling of shallower habitats (Parsley et al 1993; Paragamian et al. 2001; Rust and Wakinnen 2008, 2009, 2010; Rust et al 2010, 2011 )

Period of effects

Pre-dam and Post-dam

Mean confidence value

(3.4 of 5)

Supporting literature

Coutant 2004

Hypotheses: 

4. Stock limitation 

Description

Insufficient broodstock remain in the population to produce enough early life stages to compensate for total additive mortality in the post-development Kootenai River

Critical life stage(s)

Adults  (all life stages of future generation)

Supporting evidence

A small amount of natural recruitment is currently occurring, contributed to by a remnant population. Too few spawners remain to compensate collective mortality. (Would analogous survival rates from a population two, four, or eight times larger produce proportionally or disproportionately more recruits?)

Evidence against

A lot of populations operate successfully with much lower numbers. Historical timing of recruitment failure in the 1950s pre-dates decline of spawning stock.  Substantial numbers of adults were still present during that period based on historical stock assessments and backward projections from current numbers using estimated annual mortality rates.

Period of effects

Post-dam

Mean confidence value

(1.8 of 5)

Supporting literature

N/A

Hypotheses: 

5. Flow reduction 

Description

Recruitment failure has resulted from the effects of flow regulation on spawning and early rearing conditions 

Critical life stage(s)

Adults, and early life stages as affected by spawning location

Supporting evidence

Published positive correlations between water year (volume) and white sturgeon year class strength (Parsley et al. 1993); Observed correlations between “Larger” KR WST year classes represented from 1961, 1974, and 1991, and these years characterized by larger than average pre- and post-dam water years.

Evidence against

Periodic large flow events since 1960, including the period before and after Libby Dam construction, have produced marginal recruitment incapable of exceeding the replacement curve.

Period of effects

Post-dam

Mean confidence value

(3.4 of 5)

Supporting literature

Parsley et al. 1993; Paragamian et al. 2001; Upper Columbia WST reports

Hypotheses: 

6. Sand invasion 

Description

Post-dam hydraulics and erosion contribute to sand invasion and accumulation in the braided and meander reaches (assumed to be detrimental to spawning, incubation, and possibly survival of free embryos; strong evidence of high embryo sensitivity to sediment exposure in Kock et al. 2006).

Critical life stage(s)

Spawning, eggs, embryos, free embryos, larvae

Supporting evidence

Inability for higher post-dam discharge events to carry sand, silt, and fine sediments beyond the currently leveed channel in the meander reaches (spawning reach).  USGS observed and modeled responses to discharge effects on clearing substrate of fines in the spawning reach during high post-dam flows (e.g. 2006; Myrtle Creek area in particular) USGS KR sediment transport studies. (Barton et al. )

Evidence against

Current spawning occurs in an area of low gradient (head of large alluvial fan from braided reach) where the valley broadens and significant deposition of fine material always occurred.

Period of effects

Post-dam

Mean confidence value

No confidence (1.8 of 5)

Supporting literature

McAdam et al. 2005 (Fraser River) USGS KR sediment transport studies; Kock et al. 2006.

Hypotheses: 

7. Lack of scour 

Description

Spawning historically occurred in present spawning locations, however reduced flood flows and stream power resulting from Libby Dam operations have generally failed to clean the hard substrates of sediment or sand cover as would have occurred under historical peak flow conditions.

Critical life stage(s)

Spawning, eggs, embryos, free embryos, larvae

Supporting evidence

Inability for increased discharge events to carry sand, silt, and fine sediments beyond the currently leveed channel in the meander reach (spawning reach).

USGS measured and modeled responses to discharge effects on clearing substrate of fines in the spawning reach (Myrtle Creek area) USGS reports; Barton et al.

Evidence against

Buried substrate underneath the sand is predominantly not composed of loose rock and gravel material like that used by other successfully spawning and recruiting sturgeon populations. USGS observed removal of fines from the thalweg in Myrtle Creek area from 2006 post-dam “flood”; no year class produced.

Period of effects

Post-dam

Mean confidence value

No confidence (1.4 of 5)

Supporting literature

McAdam et al. 2005 (Fraser River); USGS KR sediment mobility reports; Barton et al..

Hypotheses: 

8. Upstream migration barrier 

Description

Some proportion of Kootenai sturgeon historically migrated upstream past Bonners Ferry to spawn in the braided and/or canyon reaches but post-dam habitat features now restrict or prohibit that historical upstream migration.

Critical life stage(s)

Adults,  and early life stages as affected by spawning location.

Supporting evidence

Failure of many fish to migrate upstream.

Evidence against

Upstream migration does occur by some fish.

Absence of imprinting to canyon reach, other reasons fish “choose” not to go upstream, or to use other habitats for spawning?

Period of effects

Post-dam

Mean confidence value

(3.1 of 5)

Supporting literature

Rust and Wakinnen 2008, 2009, 2010 Rust et al 2010, 2011

Hypotheses: 

9. Shifted hydraulic cues 

Description

Prior to levee construction and dam operation, hydraulic conditions that served as spawning cues may have existed further upstream (in the braided reach).  Today, similar hydraulic conditions may now exist downstream (in the meander reach) in the current spawning reach due to channel constriction from the enhanced levees. 

Critical life stage(s)

Adults, and early life stages as affected by spawning location.

Supporting evidence

Pre- and post-levee flow characterization.

Evidence against

Historical photos and current hydro-geomorphology work show that the hydraulic transition zone occurred much farther upstream due to the interaction of flood flows and lake backwater effects.

Period of effects

Post-dam

Mean confidence value

(3.1 of 5)

Supporting literature

USGS reports

Hypotheses: 

10. Olfactory effect on spawning location 

Description

Pheromones and chemical odorants produced by females (held in captivity to spawn at the Tribal Sturgeon Hatchery near Bonners Ferry) are released into the river via hatchery effluent and may be influencing the location where Kootenai sturgeon currently spawn (i.e., influencing the sturgeon to not migrate further upstream to spawn).

Critical life stage(s)

Adults, and early life stages as affected by spawning location.

Supporting evidence

Documented behaviors surrounding location of pre-spawning females in successfully recruiting shortnose sturgeon populations? (Boyd?).

Current spawning distribution centered longitudinally on hatchery effluent location.  Failure to migrate further upstream.

Evidence against

Very short chemical attractants (pheromones) release window associated with ovulation; KTOI’s recent review of spawning location before and after the hatchery was built, and during periods of two different hatchery effluent locations.  No correlated changes in spawning location (Shawn Young, KTOI, pers. comm.).

Period of effects

Post-hatchery (post-1990)

Mean confidence value

No confidence (1.6 of 5)

Supporting literature

Sturgeon literature, other species

image006

Figure 3. Mean confidence values (1-5) in the ability for individual hypotheses to explain recruitment failure of Kootenai River white sturgeon. Scores were averaged from surveyed responses of 20 Kootenai River White Sturgeon Recovery Team meeting participant on 3/1/12.

Recruitment failure hypotheses:

  1. Ecosystem degradation
  2. Imprinting/homing failure
  3. Riparian habitat loss
  4. Stock limitation
  5. Flow reduction
  6. Sand invasion
  7. Lack of scour
  8. Upstream migration barrier
  9. Shifted hydraulic cues
  10. Olfactory effect on spawning location

Levels of confidence:

  1 = No confidence in hypothesis

  2 = Low level of confidence

  3 = 50/50

  4 = Moderate level of confidence

  5 = High level of confidence

 

These following plots (Figure 4) portray survey results of participant confidence in each of the recruitment failure hypotheses from the recent Recovery Team attendees.

image008

Figure 4.  Confidence survey results of 10 recruitment failure hypotheses for Kootenai River white sturgeon generated at the RT meeting on 3/1/12.  The x-axis represents a 5-point confidence scale; the y-axis is the frequency of votes.

In 2007-2008, the Upper Columbia River White Sturgeon Recovery Initiative Technical Working Group undertook a year and a half long process to identify and develop a group of well-defined and broadly agreed-upon hypotheses that potentially explain the apparent recruitment failure of white sturgeon populations in the upper Columbia River.  That group used a formal structured decision-making framework and identified nearly 100 hypotheses, which were subsequently reduced to a group of 28 hypotheses.  The hypotheses were grouped under the following eight white sturgeon life stages: spawning / staging; incubation / hatching (eggs incubate for 7-10 days before hatching); pre-feeding (0-10 days) (includes both free embryo, pre-hiding stage and hiding pre-feeding stage); larval dispersal and feeding (11-40 days); young of the year (41-365 days); younger juveniles (age 1-10); older juveniles (age 11-25); and adults (age 25 and older).

A similar structured process has not been undertaken to date in the Kootenai River.  At the recent Kootenai River White Sturgeon Recovery Team meeting, attendees discussed the pros and cons of undertaking such an effort (pros: self explanatory; cons: no resources to fund it, limited time of participants, even after completing the efforts in the Upper Columbia significant uncertainties remain). 

The Tribe will continue to work with the members of the Recovery Team, co-managers, members of other sturgeon initiatives including the Columbia River Basin sturgeon coordination efforts to seek ways to better address the uncertainty regarding Kootenai sturgeon recruitment failure.  However, the remaining level of uncertainty associated with these hypotheses after so many years, and urgency to address declining Kootenai sturgeon populations, is the reason that the co-managers and experts in the Kootenai supported development of the ecosystem-based KRHRP approach.  Implementation and monitoring of the KRHRP habitat actions, of the Tribal conservation aquaculture program, and of the biological responses to the KRHRP and other restoration actions through other monitoring efforts (IDFG, nutrient program biomonitoring, and other mechanisms), will help provide information to test and refine these hypotheses.  

IV.  Summarize the history and results from the spill tests resulting from the suit by the Center for Biological Diversity (CBD) in 2003 that concerned the RPA in the 2000 Biological Opinion and the designation of Kootenai sturgeon critical habitat.

History of Critical Habitat Designation

Kootenai River white sturgeon were listed as endangered in 1994.  In 1999, the Center for Biological Diversity filed suit against the U.S. Fish and Wildlife Service (USFWS or Service) to declare critical habitat for Kootenai River white sturgeon.  The Service proposed to designate 11.2 miles river miles in the existing spawning area of the Meander Reach as critical habitat.  In comments submitted to the Service in 2001, the Center for Biological Diversity, the Ecology Center, and the Alliance for the Wild Rockies called for the decommissioning of Libby Dam to save the endangered Kootenai River white sturgeon from extinction.  Additionally, they asked the agency to increase its proposed sturgeon critical habitat area from 11.2 miles in the existing spawning reach in Idaho to include the entire Kootenai River watershed within the U.S.  The Service issued a final rule on critical habitat designation on Sept 6, 2001 designating the critical habitat described above. 

In 2003, CBD filed a complaint against the Corps and the Service stating, among other issues, that designated critical habitat for the Kootenai sturgeon was inadequate, as it failed to include areas of rocky substrate. On May 25, 2005, the District Court of Montana ruled in favor of the plaintiffs, and remanded the critical habitat designation to the Service for reconsideration.  The Service published an interim rule designating an additional reach of the Kootenai River, the braided reach, as critical habitat for the Kootenai River sturgeon in 2006, resulting in a total of 18.3 RM designated.  The critical habitat designation was finalized in 2008.

Spill Test History

The following excerpt is from the USFWS Status Review for Kootenai River White Sturgeon (Acipenser transmontanus) (Flory 2011):

“The issue of flow management in the Kootenai basin has been contentious and controversial, starting in 1995 with the issuance of the Service’s Biological Opinion on the Effects of the Federal Columbia River Power System on Five Endangered or Threatened Species (Service 1995).  That opinion contained a jeopardy conclusion for the effects of Libby Dam operations on Kootenai sturgeon.  The Reasonable and Prudent Alternative (RPA) issued in the opinion laid out a specific prescribed sturgeon flow operation at Libby Dam for the 1995 water year.  Specifically, the RPA called for peak flows during the sturgeon spawning period of full powerhouse capacity (~25,000 cubic feet per second (cfs)) plus spill of “the maximum extent possible while not exceeding total dissolved gas supersaturation in excess of state water quality standards” (110% total dissolved gas (TDG)).  The RPA also stipulated that these peak flows be maintained for 42 days.  However, releases at Libby Dam in 1995 peaked at approximately 20,000 cfs from the powerhouse (less than full capacity) and no water was spilled over the spillway.  Peak releases were maintained for 40 days.  The 1995 RPA also stipulated that in water years 1996-1998, sturgeon operations at Libby Dam consist of maximum releases from the powerhouse (25,000-27,000 cfs) and spill of “the maximum extent practicable to achieve the 35,000 cfs total discharge at Bonners Ferry”.  The RPA also required these maximum flows to be maintained for 42 days, or until sturgeon spawning had ceased.  Again however, between 1996 and 1998, the action agencies did not spill water over the spillway although the flow target of 35,000 cfs at Bonners Ferry was achieved each year.

In 2000, the Service issued a new opinion on the effects of the Federal Columbia River Power System (FCRPS), including the effects of Libby Dam operations on Kootenai sturgeon (Service 2000). Like the 1995 opinion, the 2000 opinion also reached a jeopardy conclusion for Kootenai sturgeon.  The RPA formally adopted the “tiered” sturgeon volume approach, called for sturgeon operations in excess of 25,000 cfs at Libby Dam (at least 10,000 cfs above powerhouse capacity), and called for implementation of variable flow (VARQ) flood control procedures by October 2002.  The additional 10,000 cfs was to be provided either via the spillway, or in the event the 10,000 cfs couldn’t be spilled without violating Montana’s water quality standards, via the addition of two turbines at Libby Dam.

After the issuance of the 2000 FCRPS opinion, a spill test at Libby Dam was conducted between June 25, 2002 and July 7, 2002, after most Kootenai sturgeon spawning had ceased. The purpose of the study was to evaluate the resulting TDG levels.  As the test began, unforeseen weather circumstances resulted in the operation becoming a flood control spill event, with over 15,000 cfs being spilled.  The resulting data showed that Montana’s TDG limit was exceeded at the U.S. Army Corps of Engineers (Corps) TDG monitoring station at approximately 1,600 cfs of spill (Corps 2003).

Between 2001 and 2005, sturgeon operations were managed according to the approach outlined in the 2000 FCRPS opinion, with the exception of the additional 10,000 cfs.  The 2002 spill showed that the spillway could not provide additional flows without violating Montana’s TDG standard and the action agencies did not install the additional turbines.  The post-2001 period is often referred to as the “Biological Opinion flows”, referring to the above.

In February 2003, the Center for Biological Diversity (CBD) sued the Corps for failure to implement the RPA in the 2000 FCRPS opinion.  In July 2003, the Service and the Corps agreed to reinitiate consultation and by June 2004, the District Court issued a stay of CBD’s claims pending completion of the reinitiated consultation.

On February 18, 2006 the Service issued its Biological Opinion on the Effects of Libby Dam Operation on the Kootenai River White Sturgeon, Bull Trout, and Kootenai Sturgeon Critical Habitat (Service 2006).  Like its predecessors, the 2006 opinion reached a jeopardy conclusion on the effects of Libby Dam operations on Kootenai sturgeon.  The RPA adopted a “performance based approach” in that it listed a suite of attributes that reflected the best available scientific information regarding what is necessary to adequately provide for successful Kootenai sturgeon spawning, and natural in-river reproduction.  The attributes included timing and duration of flows, velocity, temperature, depth, substrate, and frequency of occurrence. The RPA allo wed the action agencies flexibility in how to achieve these attributes. Specific to frequency of occurrence, the RPA required a flow test of 10,000 cfs above powerhouse capacity during the sturgeon spawning and migration period, in three out of the ensuing 10 years. The 2006 R PA also required the action agencies to develop a flow plan implementation protocol that addressed sturgeon flow releases.

On May 2, 2006, the Service was sued over the 2006 opinion by Center for Biological Diversity (CBD); interveners included the State of Montana and the Kootenai Tribe of Idaho (KTOI).  On September 17, 2007, the Corps was added as a defendant.  On September 2, 2008, a settlement agreement between the parties was announced.  On September 11, 2008, the Federal District Court in Missoula, MT issued an order dismissing the case.  The settlement agreement (CBD et. al. 2008) calls for the Service to clarify portions of the Libby opinion RPA.  The Service clarified the RPA on December 29, 2008 and is currently working with the parties to implement the terms of the settlement agreement.  The clarified RPA has a particular focus on Libby Dam operations in the near term (USFWS 2008).  Under the terms of the agreement and RPA, if 2008 and 2009 operations at Libby Dam for sturgeon are not deemed successful (not meeting criteria outlined in the agreement), the State of Montana will grant a waiver of their TDG standards, which will allow for spill tests to be conducted at Libby Dam in 2010-2012.  The goal of the tests is to provide additional flows to facilitate Kootenai sturgeon migration and spawning success.” (Flory 2011)

The BiOp RPA component 1.3 (see below) calls for the Action Agencies to follow the collaborative procedures for Libby Dam operations described in “The Kootenai River Ecosystem Function Restoration Flow Plan Implementation Protocol” (FPIP) developed in response to RPA Action 1.1.

a. A regional team of biologists, made up of representatives from the Kootenai Tribe of Idaho (KTOI), Confederated Salish and Kootenai Tribe, the State of Montana, the State of Idaho, the Service, and the action agencies, shall continue to collaboratively develop and assess seasonal physical and biological conditions with the objective of: (1) providing peak augmentation flows during periods the team determines appropriate based on sturgeon spawning condition (generally May into July); (2) providing post-peak augmentation flows to optimize conditions for sturgeon via the descending limb of a normalized hydrograph; and, (3) optimizing the temperature of releases using the selective withdrawal system at Libby Dam during the sturgeon flow augmentation period. This action shall be enhanced through ongoing reservoir temperature data collection and modeling efforts.

i. The Service will: consider these recommendations; develop a Systems Operations Request (SOR); and submit the SOR to the regional forum Technical Management Team (TMT) process.

ii. The Corps shall consider the SOR for implementation to benefit sturgeon, and shall implement the Service’s recommended sturgeon operation unless it determines, in good faith, that modifications are necessary due to current hydrological, biological, and operational considerations, in which case the Corps shall notify the Service immediately, and the action agencies shall utilize the regional forum process to strive for consensus on a modified operation.

b. The Service, in coordination with the regional team of biologists identified above under 1.3(a) and the action agencies, shall, in good faith, make a determination in 2008 and in 2009 as to whether interim operations at Libby Dam have been successful in providing for sturgeon reproductive and spawning needs, and will advise the action agencies of its determination. Success of the interim operations shall be determined based on the following criteria:

i. Migration of 40% of the tagged F4 fish in the river to the Hwy 95 Bridge or above; and

ii. Presence of those fish in the reach of river at or above the Hwy 95 Bridge for 5 or more days; and

iii. Capture of > 5 unmarked juveniles of the same cohort in 2009 from 2006 or 2007 year classes, when improved temperature control and a descending limb were integral components of sturgeon operations at Libby Dam.

Spill years will be similarly assessed based on the capture of juveniles 2-3 years after hatching (single year or multiple-year effort: > 5 fish in sum).  

Summary of Interim Operations and Spill Test Results

Interim Operations – Fish movement criteria i and ii and juvenile capture criteria iii:

The following summaries are compiled from reports to the USFWS from the Corps and BPA:

2008 – Criteria i and ii: Of the 26 fish that moved to and above lower Shorty’s Island in 2008, 13 were male and 13 female.  Of these fish, 56% of the fish in spawning condition detected there moved upstream to the straight reach just below Bonners Ferry, and 40% of the total detected at Shorty’s Island moved into the braided reach.  All of these fish were tagged since 2004.  Thirteen adult white sturgeon were detected in the braided reach near Bonners Ferry in late May and early June – the fourth consecutive year in which white sturgeon have been observed upstream of the Highway 95 bridge at RKM 245.9 The farthest upstream that a fish (one female) was detected was RKM 268.5. 

Criteria iii:  IDFG reported that gillnetting of juvenile (< 140 cm) white sturgeon occurred at ten sites to determine density, distribution, length frequency and age distribution of hatchery reared and wild fish.  The effort yielded more than 400 hatchery-reared and seven wild juvenile white sturgeon.  Most of the juvenile fish were collected at Rock Creek.

2009 – Criteria i and ii: Of the 17 fish that moved to and above lower Shorty’s Island in 2009, 11 were male and 6 female.  Of these fish, 12 were detected in the straight reach just below Bonners Ferry.  Two males migrated into the braided reach above the Highway 95 bridge, but no females were detected upstream.  Of the tagged spawning fish in 2009, 1 was tagged in 2003, 3 were tagged in 2005, 6 were tagged in 2006, 2 fish were tagged in 2007, and 5 fish were tagged in 2009. 

Criteria iii:  Gillnetting by IDFG personnel was conducted at random sites from Ambush Rock (rkm 244.5) downstream to near the Canadian Border to determine density, distribution, and length-frequency and age distribution of hatchery reared and wild juvenile white sturgeon.  Gillnetting in Canadian portions of the Kootenay River and Kootenay Lake was conducted by BC MOE personnel.   Gillnetting began in July and continued into September.  Over 1000 hatchery-reared and 10 wild juvenile white sturgeon were collected in Idaho and Canadian portions of the Kootenai River in 2009.  Ages will be assigned to fin rays collected from wild juveniles.    

Success Determination of Interim Operations in 2008 and 2009

After coordinating with a regional team of sturgeon biologists, the Service issued its determination of “not successful” for 2008 Libby Dam sturgeon operations on April 20, 2009, and issued a “not successful” determination for 2009 operations on December 16, 2009 (Flory 2011). 

Spill Tests – Fish movement criteria i and ii and juvenile capture criteria iii

2010 – Criteria i and ii: Of 36 tagged fish that were detected at Shorty’s Island in 2010, 28 were female and 8 were male; 16 of these fish were tagged in 2010.  Of the 7 tagged fish that moved to and above Bonners Ferry, 6 were female and 1 was male.  The male was detected at the Eagle’s Nest at rkm 250.7 in the braided reach, but no females were detected upstream of the Kootenai River Inn.  The period of fish presence above Bonners Ferry was June 4 through June 30, though presence was largely intermittent. 

Criteria iii:  Four wild juveniles were collected in Idaho portions of the Kootenai River in 2010. A section of the pectoral fin ray was removed from these four individuals for thin sectioning and age determination; two individuals were five years old (2005 year class), one individual was seven years old (2003 year class), and age could not be assigned to one individual. Three juveniles were captured near Bonners Ferry (rkm 257.0), all from upriver releases. 

2011 – Criteria i and ii: Of 27 tagged fish that were detected at Shorty’s Island in 2011, 20 were female and 7 were male; 8 of these fish were tagged in 2011.  All 4 tagged fish that moved to and above Bonners Ferry were female.  The period of fish presence above Bonners Ferry was 31 May through 03 July, though presence was largely intermittent.

 Criteria iii:  Over one thousand juvenile fish were captured during 2011, and seven wild juveniles were collected in Idaho portions of the Kootenai River. A section of the pectoral fin ray was removed from these seven individuals for thin sectioning and age determination; four individuals from the 2005 year class were captured, and one individual from each of the 2004, 2006 and 2007 year classes, respectively, were captured.

The following summary was provided by Idaho Department of Fish and Game:

“Idaho Department of Fish and Game is tasked with monitoring adult sturgeon movements using passive telemetry techniques, as well as evaluating juvenile sturgeon recruitment and status of hatchery reared sturgeon (Rust and Wakkinen 2010).  Monitoring results are presented at Recovery Team meetings and spill test success criteria are evaluated in part based on preliminary monitoring results from Idaho Department of Fish and Game. To date, preliminary monitoring results suggest that all the above criteria have not simultaneously been met in any of the spill test years.  However, at least some of the success criteria will not be able to be evaluated until several years after the tests.  Likely, a "regional team of biologists" will convene three or four years after the final spill test, scheduled for the spring of 2012, and arrive at a determination (Flory pers. comm. 2012).”

Figure 5 shows the location of the critical habitat reach relative to the Kootenai River region. 

image010

Figure 5.  Kootenai River white sturgeon critical habitat reach.

 

V.  There are three other projects on the Kootenai River that are closely related to this proposal.  Describe how this project connects with these projects.

The ISRP commented that the connections between the three Kootenai Tribe projects, and the Idaho Department of Fish and Game’s (IDFG) Kootenai River Resident Fish Mitigation project (198806500), presented as part of the resident fish, data management, and regional coordination category review, were not adequately described in any of the four proposals.  We acknowledge that this was a weakness in our collective proposals and appreciate the opportunity to better explain the relationships between these projects.  In reading through the ISRP comments on each of the four project proposals we also recognized that a more thorough explanation of the various advisory groups associated with the Tribe’s projects would also assist the ISRP in better understanding the individual projects, relationship between projects, and the Tribe’s Program as a whole. 

Towards this end the following response includes: 1) an overview of the context for the Tribe’s Fish and Wildlife Program; 2) the history of the Kootenai Tribe’s Fish and Wildlife Program; 3) a summary of the relationship of three Kootenai Tribe projects included in Resident Fish, Data Management, and Regional Coordination Category Review and IDFG’s project 198806500; 4) additional information regarding the advisory and coordination groups used to inform the Tribe’s projects; and 5) additional information regarding the subbasin-scale adaptive management plan that the Tribe is currently developing.

In many of the Tribe’s proposals mention is made of the Kootenai people’s creation story and commitment to the long-term guardianship of the land.  It can sometimes be difficult not to gloss over such statements as mere platitudes.  However, the commitment outlined in the Kootenai Tribe’s creation story is a very real and living commitment and represents the foundation from which all of the Tribe’s Fish and Wildlife Program activities emerge.

Specifically, Kootenai Tribe elders pass down the history of the beginning of time, which tells that the Kootenai people were created by Quilxka Nupika, the supreme being, and placed on earth to keep the Creator-Spirit’s Covenant – to guard and keep the land forever.  The Kootenais have never lost sight of their original purpose as guardians of the land and the Tribe’s efforts today are a reflection of this commitment.

1.  Context for the Kootenai Tribe’s Fish and Wildlife Program

As described with varying emphasis in each of the Tribe’s project proposals, over the course of the last century the Kootenai subbasin has been extensively modified by agriculture, logging, mining, and flood control.  To protect and extend agricultural and development, levees were constructed on top of natural sand levees for flood control starting in the 1900s, reducing the hydrologic connection between the Kootenai River and its floodplain.  However, without river regulation this levee system failed, or was occasionally overtopped.  The Kootenai River was confined by the construction of Libby Dam in Montana, which created Koocanusa Reservoir, and Corra Linn Dam downstream in British Columbia, which impounds Kootenay Lake.  Over 50,000 acres of historically highly productive floodplain were converted to agricultural fields, resulting in the loss of riparian and wetland plant and animal species, and the related functions that normally support a healthy ecosystem (EPA 2004).  In 1972 Libby Dam became operational, effectively reducing annual peak flows by half and disrupting the hydrograph, which historically featured a single spring freshet that provided energy to drive ecosystem processes.  These modifications resulted in unnatural flow fluctuations and changes to the temperature regime in the Kootenai River and its floodplain, which exacerbated the effects of previous anthropogenic impacts.  Construction of Libby Dam (in concert with extensive diking) also resulted in a major loss of nutrient inputs to the Kootenai River. Cumulatively, these impacts have resulted in depressed biological system productivity, altered community structure and species composition across trophic levels, and loss of floodplain and riparian function. 

The Kootenai Tribe traditionally depended on the vast aquatic and terrestrial resources of the Kootenai River subbasin and other neighboring areas (i.e., Clark Fork, Pend Oreille and the upper mainstem of the Columbia and Kootenai rivers) for subsistence and ceremonial purposes.  A natural fish passage blockage at Bonnington Falls prevented anadromous fish from entering the Kootenai River.  However, the Tribe often traveled to salmon fishing areas within the Columbia River drainage in order to take advantage of the large salmon runs in the fall of the year.  The Tribe traditionally relied upon the Kootenai River basin’s resident fish year round.  “Their chief articles of food are roots and fish.  The waters of the Kootenai River afford them at all seasons an abundant supply of salmon-trout,” reported Lt. John Mullan (1885).  Schaeffer (1940) reported “the Kutenai fished for ling in the fall/winter months using weirs constructed on tributaries of the Kootenai River”. 

While the Tribe relied on roots and fish for their main sources of food (Mullan 1885), terrestrial game and other vegetative resources were also very important for food, medicinal, spiritual and ceremonial purposes.  In addition to fish, ducks were taken in great numbers and were a staple for the Kootenai people (Turney-High 1941).  Duck netting was a communal activity with the supervision of a Duck Chief. Other waterfowl were cherished, such as geese, but these were taken by means of bow and arrow (Turney-High 1941).  Historically nearly 22,000 acres of wetland habitat were maintained by flooding river conditions throughout the Idaho portion of the lower Kootenai Valley (EPA 2004).  This large wetland area incorporated high level of energy and nutrient exchanges within the ecosystem.  Waterfowl breeding and molting seasons corresponded to flooding and subsequent wetland filling.  Avian predators once thrived in the area as well as a result of excellent habitat conditions and thriving aquatic communities.  Intact riparian areas with mature cottonwood stands contributed to provide nesting and perching habitats.

The upland terrestrial habitat supported mammals such as white tailed deer, moose, elk, woodland caribou, mule deer, and mountain goat.  Woodland caribou were an abundant resource in the Kootenai (Turney-High 1941).  The aquatic and terrestrial components of the Kootenai River ecosystem supported mammalian predators such as grizzly bears, lynx, red fox, coyote, gray wolves, cougars, fisher, river otters, mink, bobcat and black bears.

Today the ability of the Tribe to exercise Treaty-reserved fishing rights and to engage in subsistence and cultural uses of aquatic and terrestrial resources is significantly curtailed.  The local community has also suffered from the losses of diversity of aquatic and terrestrial resources that would otherwise provide an important contribution to the vitality and economic viability of the region. 

2.  Kootenai Tribe Fish and Wildlife Program Overview and History

The Kootenai Tribe’s Fisheries Department was established in 1988 and the Wildlife Division was added in 1999.  The role of the Tribe’s Fish and Wildlife Program is to work towards restoration of the Kootenai River ecosystem and implement restoration and mitigation actions that will help achieve the Tribe’s vision of: 

The Kootenai River and its floodplain as a healthy ecosystem with clean, connected terrestrial and aquatic habitats, which fully support traditional Tribal uses and other important societal uses. 

An additional component of the Tribe’s overarching vision for the Kootenai River subbasin recognizes that:

A healthy ecosystem reflects and promotes the cultural values and long-term sustainability of present and future generations.

The Tribe recognizes that implementation of this vision needs to occur within the context of a sustainable local community and economy.  In support of this approach Tribe is committed to developing and implementing innovative and collaborative approaches to shared guardianship of the land – an approach that is reflected throughout the Tribe’s Fish and Wildlife Program.  As part of their Fish and Wildlife Program activities the Kootenai Tribe also seeks specifically to restore their ability to exercise Treaty-reserved fishing rights and to assist the federal (U.S.) government in fulfilling its Tribal Trust responsibilities. 

From the outset the Tribe’s Fish and Wildlife Program has been structured around five core guiding principles: 

  • Science-based
  • Holistic
  • Collaborative
  • Consistent with Tribal cultural values
  • Inclusive of local social and economic values
  • Adaptively managed

The Tribe’s Fish and Wildlife Program grew initially out of the urgent need to address the precipitously declining Kootenai river white sturgeon population.  The Tribe’s Fisheries Department implemented the first Tribal fish and wildlife project in 1988 that included sampling of the white sturgeon population in the Kootenai River and the construction of an experimental Kootenai Sturgeon hatchery in 1991 (project 198806400).  During the late 1990s and early 2000s the impacts of declining fish populations were highlighted by a series of listing decisions and petitions to list species including Kootenai River white sturgeon (listed 1994), bull trout (listed 1998), burbot (petitioned 2000), and westslope cutthroat (petitioned 1998). 

By 1994 the Tribe and partner agencies in the Kootenai Subbasin were beginning to look beyond single species fisheries management projects and thinking about developing a more comprehensive ecosystem-based approach to investigating, identifying and addressing factors underlying the decline of native fish populations in the Kootenai subbasin.  The Kootenai River Ecosystem Restoration project (199404900), also known as the nutrient project, was started in 1994.  The project was initially an offshoot from the Tribe’s Conservation Aquaculture program (198806400), and focused on an ecosystem approach to addressing aquatic bioenergetic trophic levels and water chemistry to support fish life.  The nutrient project marked a fundamental shift in thinking at the time, from a belief that fish population declines were a stand-alone problem to be addressed, to a recognition that fish population declines were in fact symptoms of underlying ecological limitations and imbalances that needed to be addressed. 

In 1999 the Tribe added a wildlife division to the existing fisheries department and the full Kootenai Tribe Fish and Wildlife Program was created.  The Tribe’s wildlife division was added when the Tribe was incorporated into the Albeni Falls Wildlife Mitigation Project (199206105) in 1999 (although the Albeni Falls project began formally in 1992).  Inclusion in this project represented the first opportunity for the Tribe to address mitigation for wildlife losses associated with construction, inundation and operation of Albeni Falls Dam (operational losses associated with Albeni Falls Dam have not been addressed yet) and subsequently operation of Libby Dam.

The Lower Kootenai Model Watershed Restoration Project began in 2000 as a request from a landowner for help with habitat restoration work to return historical fish populations to Trout Creek, a west-side tributary to the Kootenai River.  The Tribe sought funding from Bonneville Environmental Foundation (BEF) and secured a ten-year Model Watershed restoration grant to fund a restoration and monitoring program in Trout and Long Canyon Creeks beginning in 2003 (Kruse 2007).  The majority of restoration actions have now been completed and project monitoring continues under Project 199404900.

In 2002 the Operational Loss Assessment project (project 200201100) and Reconnect project (200200800) were both added as part of the Tribe’s overall wildlife mitigation program.  The NPCC subsequently re-characterized the Reconnect project as a fisheries project and it has been included in resident fish reviews of projects.  However, the Tribe still views the primary focus and purpose of the Reconnect project as being linked to the Operational Loss Assessment and to wildlife mitigation and restoration objectives.

From the mid 1990s through early 2000s a number of regional efforts were initiated in the Kootenai subbasin that ultimately resulted in completion of recovery and/or conservation plans for Kootenai River white sturgeon, Bull Trout and Burbot.  The Kootenai Tribe was an active participant in all of the coordinated planning associated with these efforts.  Collectively these various planning efforts helped to further inform and guide the focus of assessment activities conducted under the Conservation Aquaculture project (project 198806400), Ecosystem Restoration project (project 199404900), and Assess Feasibility of Enhancing White Sturgeon Spawning Substrate Habitat project (project 200200200). 

Table 7.  Summary Kootenai Tribe Fish and Wildlife Program projects, year projects were initiated, and BPA project number.  

Year

Project

BPA Project #

1988

Kootenai River White Sturgeon Studies and Conservation Aquaculture (now titled Kootenai River Native Fish Conservation Aquaculture Program)

198806400

1992

Albeni Falls Wildlife Mitigation Project

199206105

1994

Kootenai River Ecosystem Restoration (also sometimes called the Nutrient Project)

199404900

2000

Lower Kootenai Model Watershed Restoration (funded by Bonneville Environmental Foundation)

N/A

2002

Ecosystem Operational Loss Assessment, Protection, Mitigation and Rehabilitation Project (also known as the OpLoss Project)

200201100

2002

Feasibility of Reconnecting Kootenai River with Historic Floodplain (now titled Reconnect Kootenai River with the Historical Floodplain Project)

200200800

2002

Assess Feasibility of Enhancing White Sturgeon Spawning Substrate Habitat (now titled Kootenai River Habitat Restoration Project)

200200200

The Tribe’s Fish and Wildlife Program grew initially in response to specific restoration issues and opportunities.  A more explicit identification of the framework within which the Tribe’s individual projects were nested began in 2003 with initiation of the NPCC efforts to develop standardized and collaboratively developed subbasin plans throughout the Columbia River Basin.  The Kootenai Tribe of Idaho and Montana Fish Wildlife and Parks (MFWP) took on a leadership role in this effort, producing the first complete subbasin plan in the Columbia River Basin.

The Kootenai River Subbasin Plan was completed in 2004 (KTOI and MFWP 2004).  The subbasin plan included an assessment of current conditions in the subbasin, and identified a management plan which incorporated a suite of primary and secondary limiting factors and quantifiable goals and objectives.  Figure 6 summarizes the primary and secondary limiting factors.  Figure 7 shows the role each of the Tribe’s projects plays in addressing the primary and secondary limiting factors and actions as identified in the 2004 Kootenai River Subbasin Plan (KTOI and MFWP 2004).  The Kootenai River Subbasin Plan (along with other Columbia River Basin subbasin plans) was subsequently amended into the NPCC Fish and Wildlife Program. 

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Figure 6. Primary and secondary limiting factors from Kootenai River Subbasin Plan (KTOI & MFWP 2004). 


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Figure 7.  Summary of relationship of primary and secondary limiting factors, actions (metrics/objectives from subbasin plan) and individual Tribal projects (KTOI & MFWP 2004).   

At the outset, the majority of the Tribe’s Fish and Wildlife Program projects were focused to a large extent on data collection and analysis.  Over the years as data and analysis, and monitoring and evaluation accomplished through the Tribe’s projects and through the projects of other regional partners (e.g., IDFG, MFWP, B.C. Ministry of Forest Land Natural and Resource Operations) and as the overall understanding of the Kootenai River subbasin ecosystem has improved -- the focus of the Tribe’s projects has shifted generally to more targeted feasibility analysis in support of implementation of specific restoration or mitigation actions, and to implementation of those actions.  This focus is reflected in the Tribe’s 2011 proposals. 

Another way to look at the interrelationship of the Kootenai Tribe’s Fish and Wildlife Program projects is related to how the projects address the impacts of climate, wetland disconnection and conversion, and Libby Dam hydrology on abiotic conditions, biotic communities, trophic dynamics, and species and population dynamics.  Table 8 illustrates the role that each of the Tribe’s projects plays in providing data and/or implementing actions related to each of these ecosystem components. 

Table 8.  Relationship of Kootenai Tribe projects to Kootenai River ecosystem components. 

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As part of the initial work to develop a subbasin-scale adaptive management plan for the Kootenai Tribe’s projects (discussed later) the Tribe identified five draft overarching goals that unite the Tribe’s Fish and Wildlife Program and that are consistent with broader-scale initiatives such as the Kootenai Subbasin Plan and the NPCC Fish and Wildlife Program. 

The five draft goals are to protect, restore and maintain:

  • Food web – As an oligotrophic (low nutrient) and fragmented ecosystem, the Kootenai River and its higher order organisms are likely impacted by a lack of food web support. 
  • Ecological connectivity within Kootenai River subbasin – This includes reconnecting tributaries to the mainstem Kootenai River as well as connecting the mainstem Kootenai River to riparian areas, floodplains, and terrestrial habitats.  This connection is important for nutrient exchange and will increase available habitat diversity and quantity for fish and wildlife.
  • Suitable, self-sustaining or aquatic and terrestrial habitat for fish and wildlife – Habitat is the ecosystem component that can be most directly affected by management actions such as active restoration projects.
  • Biological populations Some species in the Kootenai River ecosystem are either functionally extinct or on the verge of functional extinction. Restoring these populations, and populations of other species they depend on, is important both ecologically and culturally.
  • River physical and chemical processes, and their inherent natural range of variability – Anthropogenic activities have affected the physical and chemical processes in the ecosystem, and understanding these changes is necessary to support management actions that will address them.

All of the Kootenai Tribe projects conduct data collection, analysis or implement actions related to achieving these five goals. 

3.  Relationship of Kootenai Tribe projects included in Resident Fish, Data Management, and Regional Coordination Category Review and relationships to Idaho Department of Fish and Game project 198806500

Three Kootenai Tribe projects were proposed as part of the Resident Fish, Data Management, and Regional Coordination Category Review.  The ISRP requested a clarification of the relationships between those projects: 

  • Kootenai River Ecosystem Restoration (Nutrient Project) (199404900)
  • Reconnect Kootenai River with the Historical Floodplain Project (200200800)
  • Restore Natural Recruitment of Kootenai River White Sturgeon (Kootenai River Habitat Restoration Project) (200200200)

The ISRP also asked for clarification regarding the relationship of the three Tribal projects to the IDFG Fishery Investigations project in the Kootenai subbasin:

  • Kootenai River Fishery Investigations (Kootenai River Resident Fish Mitigation) (198806500)

The short summary to the ISRP question is that:

  • Project 199404900 (Kootenai River Ecosystem Restoration) provides nutrient addition in the Canyon Reach of the Kootenai River and Kootenay Lake in Canada, and aquatic based, trophic-level and water chemistry monitoring of a 235 km reach of the Kootenai River and key tributaries.
  • Project 200200200 (Kootenai River Habitat Restoration Project) is implementing habitat restoration actions (including mainstem, substrate enhancement, off channel, riparian, and floodplain habitats) in the Braided Reaches, Straight Reach and Meander Reaches to address the habitat needs of all life stages of Kootenai sturgeon, burbot, bull trout, kokanee, westslope cutthroat trout, and redband trout and other native fish.
  • Project 200200800 (Reconnect Kootenai River with the Historical Floodplain Project) is implementing habitat restoration to reconnect the Kootenai River with the historical Floodplain as part of wildlife habitat restoration activities associated with both the OpLoss Project and the Albeni Falls Project.  Reconnection projects identified in the 2013-2017 proposal include Ball Creek and Nimz Ranch in the Meander Reach.
  • Project 198806500 (Kootenai River Resident Fish Mitigation) is conducting monitoring and evaluation activities associated with Kootenai sturgeon and burbot that help inform recovery, habitat restoration, Libby Dam operations for sturgeon and burbot, and evaluation and adaptive management in the Kootenai River.  IDFG is also a partner to the Tribe on project 199404900 assisting with implementation of nutrient addition and monitoring the fish community at established monitoring sites throughout the basin.

The following maps are provided to help clarify the physical relationships between the projects and the extent and location of monitoring activities.  Figure 8 shows the locations of project 200200200, 200200800, 199404900 and the IDFG project 198806500 electrofishing, egg mat sites, sturgeon free embryo release sites, and sturgeon and burbot sampling sites from project 198806500.  Figure 9 shows the location of the Kootenai River Ecosystem Restoration project (199404900) course-scale and fine-scale sampling sites.  Figure 10 shows just the location of the IDFG electrofishing, egg mat sites, sturgeon free embryo release sites, and sturgeon and burbot sampling sites from project 198806500 without the other projects.

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Figure 8. Locations of Kootenai Subbasin projects 200200200, 200200800, 199404900, and 198806500.

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Figure 9. Kootenai River Ecosystem Restoration project (199404900) course-scale and fine-scale sampling sites and Kootenai River Operational Loss (200201100) avian and invertebrate sampling sites. 

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Figure 10. Idaho Department of Fish and Game (project 198806500) electrofishing sites, egg mat sites, sturgeon free embryo release sites and sturgeon and burbot sampling sites.

In the ISRP comments on the IDFG proposal and on some of the Tribe’s projects, reference was made to the various entities “claiming to coordinate”.  Something that is difficult to convey through the proposal format and to people who aren’t intimately familiar with the work in the subbasin is the extent of day-to-day coordination the occurs among the various management partners throughout the Kootenai subbasin (i.e., Kootenai Tribe, IDFG, MFWP, B.C. Ministry of Forest Land and Natural Resource Operations, U.S. Army Corps of Engineers, U.S. Fish and Wildlife Service, and Bonneville Power Administration).  We communicate regularly by email and phone, we are in meetings together, we are in workshops together, and we are in the field together on a regular basis.  The level of coordination and integration could certainly always be better but there is an extraordinary effort going into working together and continuing to learn how to work together better.

An additional factor that sometimes confounds full integration of projects is the different and occasionally conflicting organizational missions, goals and objectives among different agencies and between agencies, and the Tribe.  Additionally, the BPA/Northwest Power and Conservation Council’s review and funding process has separated wildlife and resident fish into artificially independent categories, which minimizes and obscures the integration that occurs in the real world projects. 

In the context of this resident fish review, no single action will restore populations of Kootenai sturgeon, burbot, bull trout, or other native fish in the Kootenai River.  No single entity’s actions or project(s) will restore the ecosystem.  The Tribe and other partners in the Kootenai River subbasin work together to use human and fiscal resources as effectively as possible to achieve restoration of the Kootenai River ecosystem.  This effort includes flow and temperature operations at Libby Dam (USACE and BPA in coordination with Kootenai Tribe, MFWP, IDFG and USFWS), long-term monitoring and evaluation (IDFG, BCMFLNRO, Kootenai Tribe, MFWP), habitat restoration (Kootenai Tribe, IDFG, MFWP), and critical uncertainties research (Kootenai Tribe, USACE, IDFG, MFWP).

The following sections provide additional detail regarding major actions associated with each of the three Kootenai Tribe projects and the IDFG project currently under ISRP review, and a summary of the relationships between the four projects. 

Kootenai River Ecosystem Restoration (Nutrient Addition) (199404900)

The primary goal of this project is to recover a productive, healthy and biologically diverse Kootenai River aquatic ecosystem across multiple trophic layers.  This work is important to help mitigate the effects of Libby Dam impoundment on aquatic processes in downstream river reaches.  Currently the project is implementing several nutrient restoration efforts to help mitigate 30 years of lost productivity due to Libby Dam hydro operations.

The primary objective of the project has been to address factors limiting key fish species within an ecosystem perspective.  Major project components completed include: establishment of a comprehensive and thorough biomonitoring program, investigation of ecosystem-level productivity, testing the feasibility of a large-scale Kootenai River nutrient addition experiment, the rehabilitation of key Kootenai River spawning and rearing tributaries, the provision of funding for the Canadian government for nutrient enrichment and monitoring in Kootenay Lake, providing written summaries of all research activities, and, holding an annual workshop with other agencies to discuss management, research, and monitoring strategies related to Kootenai River basin activities.  

A portion of this project is jointly implemented by the Kootenai Tribe and IDFG (the nutrient addition component for the river is a shared responsibility between the agencies).  The Tribe is responsible for the monitoring of lower trophic levels (water quality, algae and invertebrates) while IDFG is responsible for fish community data collections and analyses associated with nutrient addition in the Kootenai River.  Additionally, the Tribe purchases the nutrient supply on an annual basis and IDFG is responsible for nutrient site day- to-day management activities. IDFG, the British Columbia Ministry of Forests Land Natural Resource Operations, and the Tribe coordinate to hold an annual two day workshop center largely around the nutrient restoration efforts on the Kootenai River and Kootenay Lake, referred to as the IKERT meeting. 

Project actions include the following major components:

  • Addition of nutrients in the Idaho Canyon Reach of the Kootenai River and in the south arm of Kootenay Lake in Canada as a mitigative approach to addressing nutrient losses. 
  • A large-scale biomonitoring program covering approximately 235 km of the Kootenai River and key tributaries (in place since 2002). 
  • Targeted tributary restoration associated with Kokanee spawning habitat. 

Addition of nutrients in the Canyon Reach of the Kootenai River and in the south arm of Kootenay Lake (where Kootenai River discharges into the Lake) in Canada are being used as a mitigative approach to addressing nutrient losses.  Nutrient addition of this type are not possible in the Meander Reaches of the Kootenai River because critical environmental conditions that allow for significant primary productivity (i.e., clear, shallow water, rocky substrates) are not present in this reach.  However, nutrient effects, such as organic matter spiraling from the upriver nutrient addition zone, and fish migrations, such as kokanee spawner returns from Kootenay Lake, will likely augment trophic productivity in the Meander Reach over time.  Nutrient additions in the Canyon reach have helped reestablish the food web in the Canyon and further downstream into the Braided Reach (to a somewhat lesser degree, but still significant) since inception in 2005.  The Tribe anticipates that Canyon Reach nutrient addition will compliment habitat restoration work implemented through project 200200200 in the Braided  and Straight Reaches. 

The large-scale biomonitoring program associated with this project covers approximately 235 km of the Kootenai River and key tributaries (see Figure 9 for monitoring sites).  This biomonitoring program is designed to be sensitive to water borne nutrients, species and community level responses within the water chemistry, algal, macroinvertebrate, and fish communities.  In addition, the project developed a fine-scale biomonitoring program in 2005, specifically to monitor the effectiveness of the nutrient addition experiment in the Kootenai River.  This targeted monitoring project is collecting data on algae species dynamics and key water chemistry parameters in the heart of the nutrient addition zone to provide managers with fine-scale information for adaptive management of the nutrient project on a timely basis.

The biomonitoring program provides critical monitoring data to help measure and evaluate the biological response of habitat restoration actions conducted under projects 200200200 and 200200800 as well as supporting the Tribe’s conservation aquaculture program.  Data gathered through this biomonitoring program will also be critical to implementation of the Kootenai River Habitat Restoration Program adaptive management plan and the Tribe’s subbasin-scale adaptive management plan.   

The Tribe began a multi-year stream habitat/biota survey of lower Kootenai River tributaries (between Bonners Ferry and Porthill, Idaho) in 2000.  Similar to efforts in the Kootenai River, an ecosystem-based perspective has been used in development of monitoring plans and restoration work in tributaries.  Streams where historical kokanee salmon spawning has occurred were given top priority in the selection of tributaries segments to be restored.  The critical stream segments this project has and will continue to focus on are the area near the confluence of several key tributaries with the Kootenai River on its historical floodplain.  This tributary restoration work and the kokanee response is an important component of larger-scale efforts to enhance the Kootenai River food web.

This project addresses in river conditions only i.e., work is targeted to the aquatic ecosystem within the confines of the river banks, for the most part (some tributary riparian work has occurred and is planned).  Other Kootenai Tribe projects, specifically projects 200200800 and 200200200 will address riparian, wetland and terrestrial ecosystem habitats.

Restore Natural Recruitment of Kootenai River White Sturgeon (Kootenai River Habitat Restoration Program) (200200200)

The goal of the Kootenai River Habitat Restoration Program is to restore and maintain Kootenai River habitat conditions that support (1) all life stages of endangered Kootenai sturgeon and (2) all life stages of native focal species (i.e., burbot, bull trout, kokanee, westslope cutthroat trout, redband trout) through design and implementation of a suite of habitat restoration projects in the Braided, Straight and Meander reaches of the Kootenai River.  Building on nearly two decades of data collection and modeling related to physical habitat conditions in the Kootenai River, and on monitoring and evaluation data collected through IDFG’s project 198806500, and the Tribe’s Nutrient, Operational Loss Assessment, Reconnect, and Conservation Aquaculture projects, and the expertise of regional and local experts, the Tribe in collaboration with regional partners developed the Kootenai River Habitat Restoration Project Master Plan (Master Plan).  The Master Plan identifies limiting factors associated with river morphology, riparian habitat, aquatic habitat (including limiting factors associated with the six focal fish species), and other constraints, treatments to address those limiting factors, and restoration strategies for each river reach. 

Restoration treatments implemented through this project are designed to address: bank erosion and fine sediment inputs to downstream reaches, lack of cover for juvenile fish, lack of off channel habitat for rearing, insufficient depth for Kootenai sturgeon migration, lack of mainstem hydraulic complexity in the form of variable depth and velocity, insufficient pool frequency, simplified food web, lack of surfaces that support riparian recruitment, loss of floodplain connection, lack of coarse substrate for Kootenai sturgeon egg attachment and larval hiding, lack of bank vegetation, lack of off-channel habitat, lack of fish passage into tributaries, and grazing and floodplain land use.

Project actions are based on ecosystem restoration principles and will help to provide habitat attributes for Kootenai sturgeon that are identified in the Libby Dam Biological Opinion (implementation of the project is included in the Libby Dam settlement agreement), in addition to habitat needs for a range of life stages of burbot, bull trout, kokanee, westslope cutthroat trout, and redband trout. 

Project actions include:

  • Design and implementation of habitat restoration projects in the Braided Reaches, Straight Reach under Phase 2 (i.e., 1a and 1b extension, Bonners Ferry Islands, Straight Reach, Middle Braided 2 Meander, Lower Braided 2 Meander, Cow Creek Slough, Cow Creek, Lower Mill Slough, and Mill Slough).  Projects are designed to restore and enhance mainstem, off channel, wetland and floodplain habitat.
  • Design and implementation of a substrate addition project in the Meander Reach near Shorty’s Island (currently presented as a CAP 1135 project) where Kootenai sturgeon are currently spawning over sand and clay substrates.
  • Targeted feasibility analysis, design and implementation of 2 to 3 habitat restoration projects in the Meander Reaches under Phase 2.  Projects are designed to restore floodplain connectivity and off channel habitat in the Meander Reaches with a focus on aquatic species.  This project compliments work for terrestrial communities, but will not address wildlife mitigation or terrestrial objectives.
  • Development and implementation of monitoring and evaluation plans for each individual Phase 2 and Phase 3 project.
  • Implementation of the Kootenai River Habitat Restoration Program adaptive management plan.

Data and analysis to support development of the project Master Plan, concept designs for Phase 2 and Phase 3, and development of preliminary and final designs for all projects has, and will continue to, incorporate data collection and analysis associated with the Nutrient project and Reconnect project (as well as the Operational Loss Assessment project).  Information collected through IDFG monitoring and evaluation activities for Kootenai sturgeon and burbot was also used to support development of the Master Plan, concept designs for Phase 2 and Phase 3, and development of preliminary and final designs is provide through the data collection and analysis associated with the Nutrient project.  The Tribe is coordinating with IDFG, MFWP and other partners (i.e., BCMFLNRO, USACE, USFWS, BPA) to incorporate the most recent data and analysis in each stage of the project design process.  IDFG participates in the Co-manager and Agency Team (CMART) that has helped develop and review the suite of projects proposed under this project and is coordinating with the Tribe to refine the monitoring and evaluation associated with each project as it is designed. 

Biological monitoring and evaluation to determine the biological response to the habitat restoration projects (i.e., 1135 project, and Phase 1, Phase 2 and Phase 3 projects) will be conducted by IDFG under their project 198806500.  The Tribe is coordinating directly with IDFG to review monitoring and evaluation associated with individual projects as those projects are developed.  The Tribe coordinated with IDFG to conduct pre- and post-project side channel monitoring in support of the Phase 1a and 1b projects implemented under this program in 2011.  The Tribe will supplement the IDFG sturgeon and burbot monitoring with additional side channel monitoring in 2012 and is also coordinating with IDFG on development and design of additional side channel monitoring plans.

Information collected through the Nutrient project’s (199404900) biomonitoring will also be used to help measure the biological response to the suite of habitat restoration projects at various trophic levels and among other fish communities.

IDFG and the program managers for the Tribe’s Nutrient project, Reconnect project and Operational Loss project are also participants in this projects Core Adaptive Management Team which will assist in review and analysis of monitoring and evaluation information and in implementation of the project adaptive management plan.

Reconnect Kootenai River with the Historical Floodplain Project (200200800)

The primary goal of the Reconnect project is to investigate and implement actions that enhance terrestrial and lentic habitats by reconnecting the Kootenai River with its historical floodplain in the Kootenai River.  This project was originally categorized as a wildlife habitat restoration project and the project was closely linked to work conducted under the Albeni Falls Wildlife Mitigation Project (199206100) and the Operational Loss Assessment Project (200201100).  The Oploss Project is developing the framework to assess and monitor reconnection opportunities.  Each reconnect or mitigation project can be folded back into the ecological framework developed by the Oploss Project to assess cumulative impacts of multiple projects over time.  Floodplain reconnection activities under this project are purposely associated with the Tribe’s wildlife mitigation program to ensure long-term protection and designed to address both lentic and terrestrial objectives.  Under this project the Tribe has examined the feasibility of reconnecting floodplain habitats with the mainstem in the Meander Reaches of the Kootenai River.  Since 2002, this included identification and initial assessment of the feasibility of reconnecting six tributary/wetland complexes to the mainstem Kootenai River. 

Project actions include the following major components:

  • Complete design, permitting and implementation of the Ball Creek Stream Restoration project.  
  • Complete other floodplain reconnection activities in association with the Albeni Falls Wildlife Mitigation Project (199206100) and the Operational Loss Assessment Project (200201100). The Reconnect Project will initiate reconnection/restoration activities on a newly acquired property under the Albeni Falls project (Nimz Ranch). 
  • Develop a restoration ranking plan for floodplain/wetland reconnection, restoration and wildlife mitigation opportunities.
  • Explore opportunities to create biologic, social, and economic benefits using flood/groundwater storage and implement pilot project.
  • Assess floodplain ecosystem restoration effectiveness and inform prioritization process by implementing adaptive management process.  This includes implementing invasive species control management techniques in floodplain habitats and developing a study plan to assess interaction of trophic and nutrient dynamics between restored floodplain lentic systems and the Kootenai River.

In addition to supporting feasibility assessment work for Ball Creek and completing initial feasibility analysis for reconnecting six other tributary/wetland complexes in the Meander Reaches, LiDAR data collected as part of this project has helped develop a 2D hydrodynamic model that is used to assess Libby Dam hydraulic impacts, model vegetation succession, and simulate restoration effects to the floodplain under the Oploss Project along with supporting development of the Kootenai River Habitat Restoration Program Master Plan and conceptual design of projects to be implemented under project 200200200.

This project will complement and augment habitat restoration work planned in the Meander Reaches under Phase 3 of project 200200200 by creating conditions that help support an enhanced food web, and contribute to a more complex and diverse terrestrial habitat communities for a variety of wildlife focal species and aquatic species.  An important aspect of the Reconnect Project is that it purposefully focuses on wildlife mitigation in the Kootenai River floodplain to ensure long-term protection and enhancement opportunities.  Moreover, the Reconnect Project targets floodplain biotic communities identified by Oploss Project assessments with an emphasis on the intersection between aquatic and terrestrial connectivity.  The complimentary work conducted under project 200200200 will be addressing sturgeon and other focal species (e.g., burbot, kokanee, etc.) mitigation restoration opportunities in the Meander Reaches and focusing primarily on aquatic/riparian restoration objectives.

Biomonitoring data conducted under the Nutrient project (199404900) are used to help inform project design and will help measure the biological benefits of this project.

Kootenai River Fishery Investigations (Kootenai River Resident Fish Mitigation) (198806500)

While the three Kootenai Tribe projects in this proposal cycle (199404900, 200200200 and 200200800) are largely focused on completion of targeted feasibility assessment and implementation of actions to restore habitat (e.g., nutrient addition, mainstem restoration, side-channel restoration, tributary and floodplain reconnection), the Kootenai River Resident Fish Mitigation project (in coordination with biomonitoring conducted under 199404900) is the monitoring backbone that supports the design, monitoring and adaptive management of the various restoration projects.  The Kootenai River Resident Fish Mitigation project is composed of several studies specifically focused on the recovery of white sturgeon (ESA listed), burbot, and salmonid fisheries.

Project actions include the following major components:

  • Monitor spatial and temporal distribution of Kootenai sturgeon spawning events, early May through mid-July by collecting sturgeon eggs on artificial substrates (egg mats).
  • Monitor and evaluate Kootenai sturgeon vital statistics in response to recovery.
  • Monitor and evaluate juvenile and adult burbot population dynamics.
  • Monitor and evaluate burbot early life survival strategies.
  • Monitor and evaluate salmonid vital statistics in response to recovery strategies.
  • Co-manage and evaluate nutrient restoration program.

This project provides monitoring and evaluation to help better understand Kootenai sturgeon response to flow and temperature management operations implemented by the USACE and BPA (in coordination with other partner agencies) and to help inform regional decision-making processes regarding future operations.

This project provides monitoring and evaluation that is helping develop design criteria for Kootenai sturgeon and burbot for the Kootenai Tribe’s project 200200200 including design of the Phase 1, Phase 2, Phase 3 and 1135 projects.

This project provides monitoring and evaluation of Kootenai sturgeon and burbot that will be used to help evaluate, in coordination with information collected through the Tribe’s biomonitoring sites (199404900), the biological response to actions implemented under project 200200200. 

Information developed through this project is used to inform discussions and recommendations developed in the Kootenai River White Sturgeon Recovery Team, Burbot Conservation Committee, Libby Dam Flow Policy and Technical Teams, and the Tribe’s various technical and expert advisory groups (see subsequent discussion).

IDFG is also a partner to the Tribe on project 199404900 which helps support ecosystem restoration through nutrient addition as well as the extensive biomonitoring project.

4. Technical advisory teams, coordination mechanisms, and other critical outreach

A critical element of many of the projects within the Tribe’s Fish and Wildlife Program is the use of technical advisory teams to provide expert technical advice and critical review at various stages of each project.  Not every expert is an expert on every topic .  To address the need for a rigorous and timely level of review and/or design analysis on various projects and to be sure we get interdisciplinary input, a number of the Tribe’s projects have identified specific teams of technical experts representing a range of disciplines specific to the needs of each project (e.g., river restoration implementation or hydraulic engineering, etc.).  These groups fulfill different roles on each of the projects but in all cases are used to enhance the quality of the projects and provide independent review and input at critical junctures.

It was clear from the ISRPs comments that our presentation of the role and purpose of the different groups relative to different Tribal projects was confusing.  For example, in order to make the best use of these expert resources, and in order to assist in integration and information sharing between projects, groups that provide a technical advisory/oversight role for one project (e.g., IKERT for the Nutrient project) may serve as stakeholder outreach or coordination for another project (e.g., Habitat restoration project). 

Following is a summary of the major advisory teams that have been assembled for the Tribal projects that make use of them.  Table 9 summarizes the different technical oversight or advisory groups, stakeholder or educational outreach and other complimentary coordination mechanisms associated with each project. 

Table 9.  Summary of Kootenai Tribe project technical oversight and/or advisory groups, stakeholder or education outreach and other complimentary coordination associated with each project. 

Project Number

Project Name

Project Specific Technical Oversight and/or Advisory Group

Stakeholder Outreach and/or Education Group(s)

Other Critical Coordination

198806400

Conservation Aquaculture

KRWSRT

BCS

KVRI

IKERT

IDFG

MFWP

BCMFLNRO

199206103

Albeni Falls

AFIWG

KVRI

DU

IDFG

UCUT

NRCS

199404900*

Nutrient Addition

IKERT

IDFG (partner)

TU

KVRI

RDRT

BCC

MFWP

BCMFLNRO

200201100

Op Loss

RDRT

IKERT

RDRT

CMART

KVRI

IDFG

MFWP

200200800*

Reconnect

N/A

IKERT

RDRT

CMART

KVRI

TNC

IDFG

 

200200200*

Habitat Restoration

PRAT

CMART

KRHRP PT

CAMT

IKERT

KVRI

KRWSRT

BCS

Community outreach

IDFG

MFWP

BCMFLNRO

Landowners

NRCS

State and Federal agencies

 

  • AFIWG =Albeni Falls Interagency Working Group
  • BPA = Bonneville Power Administration
  • BCS = Burbot Conservation Subcommittee
  • BCMFLNRO = British Columbia Ministry of Forest Land Natural Resource Operations
  • CAMT = Core Adaptive Management Team (200200200)
  • CMART = Co-manager/Agency Review Team (200200200)
  • DU = Ducks Unlimited
  • IDFG = Idaho Department of Fish and Game
  • IKERT = International Kootenay/I Ecosystem Recovery Team (199404900)
  • KRWSRT = Kootenai River White Sturgeon Recovery Team
  • KVRI = Kootenai Valley Resource Initiative
  • MFWP = Montana Fish Wildlife and Parks
  • NRCS = Natural Resources Conservation Service
  • KRHRP PT = Policy Team (200200200)
  • PRAT = Peer Reviewer Advisory Team (200200200)
  • RDRT = Research Design and Review Team (200201100)
  • UCUT = Upper Columbia United Tribes
  • USACE = U.S. Army Corps of Engineers

* Projects that are part of this ISRP review.

 

Following is a summary of the major advisory groups associated with each of the Tribe’s projects.  Where appropriate, membership details are provided for the unique expert technical groups to help illustrate the specific suite of technical expertise that has been assembled to help guide the projects.

Kootenai River Ecosystem Restoration (BPA Project 1994-049-00) 

Technical Review Group: International Kootenay/i River Ecosystem Restoration Team (IKERT)

Purpose:  Annual IKERT meetings have occurred since 2000 and have played an important role in organizing and directing activities for this project.  The IKERT group assists with presenting, analyzing, and discussing monitoring and research data collected by Tribal staff and project contractors to meet project objectives.  During the past decade, the group has been heavily involved in review of the nutrient and productivity technical aspects of the project, both for the Kootenai River and Kootenay Lake.  The group has played an important role in designing the Tribe’s trophic level and water quality Biomonitoring program, and nutrient addition feasibility, testing, and implementation. 

Group composition:  All parties involved in the management and/or research of the Kootenai River ecosystem are regularly invited to attend the IKERT annual meeting.  Currently representatives from Kootenai Tribe, Bonneville Power Administration, IDFG, MFWP, British Columbia Ministry of Forests Land Natural Resource Operations, the University of Idaho, Idaho State University, and the University of British Columbia attend IKERT functions during most years.  Table 10 lists the IKERT representatives.  

Table 10.  Core representatives of International Kootenay/i Ecosystem Restoration Team. 

Name

Expertise

Affiliation

Bahman Shafii, Ph.D.

Statistician/ Science Advisor  

University of Idaho

Cathy Gidley, MS

Nutrient Site Manager/Fisheries

Idaho Dept. Fish and Game

Charlie Holderman, MS

Project Management/ Aquatic Ecology

Kootenai Tribe of Idaho

Eva Schindler, BS

Limnologist, Project Manager, Kootenay Lake Nutrient Addition

British Columbia Ministry of Forests Land Natural Resource Operations

Gary Lester, BS

Macroinvertebrate Ecology

EcoAnalysts, Inc.

Genny Hoyle, MS

Project Field Monitoring/ Aquatic Ecology & Water Chemistry

Kootenai Tribe of Idaho

Gretchen Kruse, MS

Large River Ecology

Free Run Aquatic Research

Greg Hoffman, MS

Fisheries/ Kootenai River Hydraulic Operations

Army Corps of Engineers

Greg Andrusak, MS

Fisheries

Redfish Consulting

Harvey Andrusak, MS

Fisheries/ Kokanee, Trout Ecology

Redfish Consulting

Hassen Yassien, Ph.D.

Civil/ Hydraulic Engineer

Ward and Associates, LTD

Jeff Laufle, MS

Fisheries/ Columbia Basin Hydraulic Operations

Army Corps of Engineers

Jeff Burrows, MS

Administration

British Columbia Ministry of Forests Land Natural Resource Operations

Ken Hall, Ph.D.

Water Chemistry

University of British Columbia, Retired Professor

Ken Ashley, Ph.D.

Aquatic Ecology/ Nutrient Addition Expert

University of British Columbia

Jim Dunnigan, MS

Manager/ Fisheries

Montana Fish Wildlife and Parks

Kevin Greenleaf, BS

Environmental Director/ Invasive Species

Kootenai Tribe of Idaho

Lee Watts, BS

Project Administration

Bonneville Power Administration

Nancy Leonard, Ph.D.

Science Advisor

Northwest Power Planning Council

Norm Merz, MS

Manager/ Wildlife Ecologist

Kootenai Tribe of Idaho

Paul Anders, Ph.D.

Senior Fisheries Scientist

Cramer Fish Sciences, Inc.

Peter Ward, Ph.D.

Hydraulic Engineer

Ward and Associates, Inc.

Ryan Sylvester, MS

Aquatic Ecology/ Didymosphenia Researcher

Montana Fish Wildlife and Parks

Ryan Hardy, MS

Principle Fisheries Manager, North Idaho

Idaho Department of Fish and Game

Sue Ireland, MS

Fish and Wildlife Director

Kootenai Tribe of Idaho

Wayne Minshall, Ph.D.

Aquatic Ecology Expert

Idaho State University, Retired Professor




 

 


 

 


 



 

 


 

 

 

 

 

 

 

 

 

 

 

Frequency of meetings and/or other coordination:  The larger group meeting (all members) occurs once per year, typically in the spring.  This allows for review of the previous year’s data and to make adjustments prior to the nutrient addition and biomonitoring seasons.  Smaller sub-group meetings occur throughout the year.  One such group is the IKERT nutrient sub-committee which meets via conference call 1-2 times per month during the nutrient addition season (June-Sept.).  Other smaller meetings include discussions concerning sampling designs, sample size, sampling frequency, data analyses, and report and manuscript development occur on approximately a quarterly basis throughout the year.   

Purpose of meetings and/or other coordination:  The primary purpose of the IKERT meetings is to present and review project results within a technical workgroup setting that allows for the interchange of ideas and improvements.  Additionally, the group discusses ecosystem restoration ideas and techniques, and provides a forum for presenting information about related topics in other river systems and other inter-related Kootenai River projects.

Other desired outcomes include technical analyses and input on technical issues, such as nutrient limitation evaluations, that can be used by tribal management for decision-making and adaptive management.  For example this group was responsible for evaluating biological and water chemistry data and making a recommendation to the Tribe and Idaho Dept. of Fish and Game regarding whether to add or not add nutrients to the Kootenai River in 2004.

At times, the IKERT meeting will be combined with an Adaptive Environmental Assessment (AEA) workshop to plan and coordinate all Kootenai River Projects in the Idaho reaches of the river.  This allows for a "big-picture" view of fish and wildlife projects in the subbasin and how to best coordinate them to recover the Kootenai River ecosystem.  These have typically occurred on a 5-year basis.  As the Kootenai Tribe’s subbasin-scale adaptive management plan moves forward to completion we will review coordination with the AEA workshop.

Kootenai River Floodplain Ecosystem Operational Loss Assessment, Protection, Mitigation and Rehabilitation Project (BPA Project 200201100)

Technical Review Group: Research Design and Review Team (RDRT)

Purpose:  The purpose of the RDRT is to provide input, reviews, and critiques of project methodology, implementation, analyses results, and interpretation.  The RDRT helps to incorporate this information into the Operation Loss Assessment.

Group composition: RDRT includes invited experts from a range of relevant disciplines including terrestrial wildlife ecology, floodplain and vegetation ecology, wetland ecology, invertebrate ecology, hydrology, Libby Dam operations, modeling expertise, etc.  Table 11 presents the RDRT members.

Table 11. Research Design and Review Team (RDRT) participants. 

Name

Expertise

Affiliation

Alan Wood, Ph.D.

Terrestrial wildlife ecology

Montana Fish Wildlife and Parks

Arpine Jenderedjian

Floodplain vegetation ecology/modeling

Umweltbuero Klagenfurt, Austria

Bahman Shafii, Ph.D.

Statistics

Statistical Consulting Services

Brian Bieger, MS

Wetland ecology

Interfluve Inc.

Dwight Bergeron, MS

Terrestrial wildlife ecology

Montana Fish Wildlife and Parks

Elowyn Yager, Ph.D.

Hydrology/Hydraulic/modeling

University of Idaho

Karen Gill, MS

Riparian vegetation ecology

University of Lethbridge

Gregory Egger, Ph.D.

Floodplain vegetation ecology/modeling

Umweltbuero Klagenfurt, Austria

Greg Hoffman

Libby Dam operation

U.S. Army Corps of Engineers

Mike Burke, MS

Hydrology/Hydraulic

Interfluve Inc.

Norm Merz, MS

Project Manager

Kootenai Tribe of Idaho

Paul Anders, Ph.D.

Aquatic ecology

Cramer Fish Sciences

Phil Tanimoto, Ph.D.

GIS analyst

Texas A&M, College Station, TX.

Rohan Benjankar, Ph.D.

Hydrology/Hydraulic/modeling

University of Idaho

Tim Hatten, Ph.D.

Invertebrate ecology

Invertebrate Ecology Inc.

Scott Soults, BS

Project Manager

Kootenai Tribe of Idaho

Stewart Rood, Ph.D.

Riparian vegetation ecology

University of Lethbridge


 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Frequency of meetings and/or other coordination:  The RDRT and RDRT subgroups are convened as necessary at appropriate times during the development of methods and/or review results of analyses.  Typically, a subgroup is convened at least quarterly, with a full group meeting occurring annually.

Purpose of meetings and/or other coordination:  The purpose of the annual meeting and quarterly subgroup meetings is to inform, discuss, review, critique and recommend project related activities and direction.

Kootenai River Habitat Restoration Project (BPA Project 2002-002-00)

Technical Review Groups: Peer Reviewer Advisory Team (PRAT), Co-manager/Agency Review Team (CMART), Kootenai River Habitat Restoration Program Policy Team (KRHRP PT), Modeling Review Group, and Core Adaptive Management Team (CAMT).

Peer Reviewer Advisory Team (PRAT): The purpose of the Peer Advisory Review Team (PRAT) is to provide additional depth of expertise to the Tribe’s design team.  The PRAT assists in development and review of design concepts, preliminary designs and feasibility analysis, and final design. PRAT members are also available on an on-call basis to provide specific input into development of design criteria, review or interpretation of modeling outputs, or one-on-one assistance with design components.  The design team has made regular use of PRAT members in this capacity, seeking advice on subjects such as development of a literature review of salmonid habitat requirements, assistance in development of side channel design criteria, a site visit to the lower Columbia River to view and interpret sturgeon spawning habitat characteristics with a local expert, and review of structural feasibility of design components in the Phase 1a and 1b projects.  Table 12. summarizes the PRAT representation.

Table 12. KRHRP Peer Reviewer Advisory Team (PRAT) representatives.

Name

Expertise

Affiliation

Dr. Janine Castro

Geomorphology and river restoration

USFWS and Technical Director of the Portland State University River Restoration Professional Certificate Program

Gary Decker

Design and implementation of stream restoration projects

WestWater Consultants, Inc.

Bill Fullerton

Hydraulics and geomorphology and their application to civil engineering and environmental projects

Tetra Tech, Inc.

Duncan Hay (Dip. H.E.)

Engineering, hydraulic structures, environmental hydraulics and hydraulic modelling

Oakwood Consulting, Inc.

Larry Hildebrand

Sturgeon biology and research in upper and middle Columbia River and lower Fraser River

Golder Associates Ltd.

Dr. Boyd Kynard

Sturgeon behavior, early life stage research on Kootenai sturgeon

B.K. River Fish

Mike Parsley

Sturgeon ecology and biology, and sturgeon habitat assessment

USGS Western Fisheries Research Center, Columbia River Research Laboratory

Dr. Jon Nelson

Sediment-transport mechanics and computational modeling of flow and sediment transport in rivers

U.S. Geological Survey

Dr. Stewart Rood

Ecology

University of Lethbridge

Dr. Brad Shepard

Salmonid biology and research

Wildlife Conservation Society.

 

 

 

 

 

 

 

 

 

 

 

 

Frequency of meetings and/or other coordination: The PRAT meets formally on average twice a year for two-day workshops and is also available on call to provide input and review on an as needed basis.

Other advisory Kootenai River Habitat Restoration Project technical groups

Co-manager and Agency Review Team (CMART): The Tribe established the CMART to provide a venue for discussion, review of design concepts and preliminary and final design. The intent was to ensure comprehensive information sharing among the co-managers and agency partners who are working in the Kootenai subbasin, and also the Federal agencies who have legal obligations under the ESA and Tribal Trust with the project design team. The primary purpose of this group is to ensure that best available science is incorporated into the development, design and implementation of restoration projects and that projects are developed in a collaborative manner.

Participants include technical representatives from: Idaho Department of Fish and Game (IDFG), Montana Department of Fish Wildlife and Parks (MFWP), B.C. Ministry of Forests Land Natural Resource Operations (BC MFLNRO formerly BC Ministry of Environment), U.S. Fish and Wildlife Service (USFWS), U.S. Army Corps of Engineers (USACE), U.S. Geological Survey (USGS), BPA, Kootenai Tribe (including program managers for other projects), and University of Idaho.  This group also includes the Kootenai River White Sturgeon Recovery Team members, individuals involved in implementation of the Burbot Conservation Strategy, and project managers for the Tribe’s other ecosystem restoration projects (e.g., Operational Loss, Reconnect, and Ecosystem).

Core Adaptive Management Team (CAMT): The CAMT includes many participants from the CMART but the purpose of this group is specifically to review monitoring and evaluation plans for individual projects, and participate in annual adaptive management reviews of the KRHRP. The Tribe will also use the CAMT as a mechanism to ensure coordination with monitoring and evaluation activities conducted by co-managers (e.g., IDFG, BC MFLNRO, MFWP) to better understand the effect of KRHRP projects on focal populations. In the future, as the project progresses, the Tribe may recruit additional expertise to this team to assist in review and interpretation of KRHRP monitoring and evaluation information.

Modeling Review Team: The Tribe has also established a modeling review team, which includes the Tribe’s design team members, and representatives from USGS and USACE (and others as appropriate). The purpose of this group is to review model outputs and interpretations, validate and identify potential adjustments to models, and coordinate efforts to eliminate duplication of effort.

Policy Team: The Tribe also established a Kootenai Habitat Policy Team to help provide policy guidance for the project and to help support effective interaction between policy level agency representatives and field staff. Policy Team members include appointed policy level representatives for the USACE, BPA, USFWS, states of Idaho and Montana, and Confederated Salish and Kootenai Tribes.  NPPC members and staff have also regularly attended Policy Team meetings.

Other major coordination and outreach forums in the Kootenai River subbasin that influence all of three Kootenai Tribe and one IDFG proposal contained in this review.

The following additional coordination and outreach forums play a critical role in the coordination and integration of ecosystem restoration efforts in the Kootenai River.  This information is provided to assist the ISRP in understanding some of the other avenues through which project actions are coordinated.

Kootenai Valley Resource Initiative:  The Kootenai Tribe of Idaho, the City of Bonners Ferry, and Boundary County are working together to address resource issues affecting the Lower Kootenai subbasin. The Kootenai Valley Resource Initiative (KVRI) was formed under a Joint Powers Agreement between the Tribe, the City of Bonners Ferry, and Boundary County in October 2001 to foster community involvement and development in the restoration and enhancement of the resources of the Kootenai Valley.  The initiative includes membership and partners that represent the broad diversity of the community.  The group has been meeting monthly for over ten years.

KVRI is a proactive forum for the community to bring key players to the table, build connectivity between the community and the agencies for information sharing and exchange, as well as to use partnerships and a collaborative approach for community involvement in restoration efforts.  KVRI meets monthly and we use this forum to provide the KVRI board members, agency partners, and community members with information and periodic updates about our projects at key intervals during project implementation.  Additionally, subcommittees can be formed (with the approval of the KVRI board) to address a specific subject or issue in more detail.  Please see information about KVRI subcommittees and how our projects have used them below.  KVRI has also assisted with hosting broad scale public outreach meetings for our projects, as well as the outreach for the development of the Kootenai Subbasin Plan.

KVRI Co-Chairs include Kootenai Tribe of Idaho Tribal Chairperson, Boundary County Commissioner, and Mayor of Bonners Ferry.  KVRI Board Member Representatives include: landowner (Industrial), business/industry, conservationist, soil conservation district/ag landowner, corporate agriculture/landowner, U.S. Forest Service – Idaho Panhandle National Forest, Idaho Fish and Game Commission, and social/cultural/historical.

In addition to the board members, KVRI includes many partners.  KVRI partners include a diverse group of local, state and federal agencies, non-profit organizations, congressional representatives, and community members.  Project outreach occurs at least annually through KVRI and more frequently on an as-needed basis.

KVRI Burbot Subcommittee: Due to changes in the ecosystem over the last century, the burbot in the Lower Kootenai River had collapsed and was proposed for listing.  Through the Burbot Subcommittee of the KVRI, the Tribe facilitated a collaborative process to prepare and implement a conservation strategy to restore the burbot population.   An MOU developed to confirm commitment and guide implementation of the conservation strategy was signed by 16 agencies and entities. By building consensus through the development of the conservation strategy, actions needed to restore burbot and the habitat upon which it depends maintains strong community and agency support. The Tribe coordinates with the KVRI Burbot Subcommittee to gain community input for the support and implementation of this transboundary effort.

The KVRI Burbot Subcommittee includes over 30 members including action agency and co-managers, representatives from non-profit organizations, and community members.  The group meets a least semi-annually to coordinate and review progress.  

KVRI Total Maximum Daily Load (TMDL) Subcommittee: This group was developed in response to an MOA between Kootenai Tribe of Idaho, Idaho Department of Environmental Quality and EPA region10, and the need to coordinate with City and county governments in association with the designation of this committee as a Watershed Advisory Group (WAG) by Idaho DEQ.  The group deals with: Subbasin assessment; load allocation, analysis and implementation; BMP’s for restoration; coordinating partners and responsibility; and looking at new approaches to Temperature TMDL (i.e., potential natural vegetation).

The KVRI TMDL Subcommittee includes 15 members including citizens, county government, Kootenai Tribe, State, Idaho DEQ, farmers, Natural Resources Conservation Service, NGOs, environmental representatives, and the county soil conservation district.  The subcommittee meeting quarterly.

KVRI Wetland/Riparian Subcommittee: This subcommittee developed a reference report for the Tribe, agencies and others to use documenting a decision-making process regarding wetlands and riparian areas in the Kootenai Valley.  The purpose of the group is to balance social, natural resources and economic perspectives; coordinate purchase and restoration of wetlands; work in partnership with IDFG and associated Wildlife Management Areas, and conduct education and outreach.

The KVRI Wetland/Riparian Subcommittee includes 15 to 20 members including citizens, county government, Tribe, IDFG, farmers, USFS, Natural Resources Conservation  Service, NGOs, environmental representatives, county soil conservation district, and forestry, agricultural, industrial representatives.  The group hasn’t met since 2006.  The report resulting from the group’s effort is available at: http://restoringthekootenai.org/resources/F&W-Library/Wildlife/7WL-Final-WRCS.pdf)

KVRI Grizzly Bear Conservation Subcommittee: This subcommittee serves as a forum to disseminate natural resource information, educate community on grizzly bear management and to determine management opportunities.  The purpose of the group is to enhance understanding of grizzly bear life history, population trends/genetics, and habitats needs. 

The KVRI Grizzly Bear Conservation Subcommittee includes 25 members including citizens, county government, Tribe, IDFG, farmers, USFS, Natural Resources Conservation  Service, NGOs, environmental representatives, county soil conservation district, and forestry, agricultural, industrial representatives.  The subcommittee meets quarterly.

KVRI Wildlife Auto-Collision Subcommittee:  This subcommittee serves as a conduit for reaching out to the community for feedback and guidance in considering ways to reduce wildlife conflicts and building support for transportation mitigation efforts.  The purpose of the subcommittee is to implementation of consensus based strategies, identify and increase line-of-sight in area hot spots, collect data to identify hotspots and hotspot changes due to development, and assist with the wildlife crossing database.

The KVRI Wildlife Auto-Collision Subcommittee includes 30 members including citizens, county government, Tribe, IDFG, Idaho Transportation Department, USFWS, USFS, NRCS, US Federal Highways Administration, forestry, agricultural, industrial representatives and NGO environmental representatives.  The subcommittee meets once or twice a year.

KVRI Forestry Subcommittee:  The subcommittee works to enhance understanding and help address federal forest resource issues with the community, including and base planning and coordination using a landscape approach.  The purpose of the is to approach decision making process with a balanced approach and make lands economically, ecologically and socially sustainable, use science-based approaches, develop common ground for natural resource managers and community alike, develop grants for additional restoration opportunities and provide education and outreach.

The KVRI Forestry Subcommittee includes 30 members and includes citizens, county government, Tribe, IDFG, Idaho Transportation Dept., USFWS, USFS, NRCS, loggers, forestry, agricultural, industrial representatives and NGO environmental representatives.  The subcommittee meets quarterly.

Libby Dam Flow Policy and Technical Teams:  Libby Dam flow management coordination, as it relates to BiOp requirements, occurs through the USFWS BiOp/Libby Dam Operations Regional Flow Policy Team coordinated by the USACE.  The Policy Team assigns a Technical Team to summarize the biological and physical considerations for a policy decision regarding sturgeon flow and temperature management at Libby Dam each year. The recommendation is prepared with the specific intent of achieving the requirements of clarified RPA 1 Action 1.5, along with the physical attributes in the Kootenai River thought to positively influence sturgeon spawning success. Success of obtaining certain habitat attributes implemented by the KRHRP will take place in this forum, as well as the USFWS white sturgeon recovery team.  

Group participants include the Federal action agencies and co-managers (BPA, USACE,
USFWS, Kootenai Tribe, IDFG, MFWP).  The group meets annually in the spring to develop and approve flow recommendations for implementation during the sturgeon spawning season.

Kootenai River White Sturgeon Recovery Team:  The Kootenai River White Sturgeon Recovery Team is convened by the U.S. Fish and Wildlife Service.  The Recovery Team shares information and analysis regarding Kootenai sturgeon population status, monitoring and evaluation, research work, habitat restoration initiatives, and provides advice to the U.S. Fish and Wildlife Service.  The group also functions as a forum to review and discuss habitat restoration projects, the Tribe’s Conservation Aquaculture program, etc. 

The KRWSRT is lead by the U.S. Fish and Wildlife Service and includes appointed representatives from BPA, MFWP, IDFG, USACE and BCMFLNRO.  In addition to the formal membership, KRWSRT meetings are attended by a broad range of experts including members of the Upper Columbia River White Sturgeon Recovery Initiative Technical Working Group, sturgeon experts, and representatives of stakeholder groups.  Kootenai River White Sturgeon Recovery Team meetings occur two to three times a year.

5.  Kootenai Tribe’s Kootenai River Draft Subbasin Scale Adaptive Management Plan. 

In a number of the ISRP responses to the Tribe’s projects, the ISRP requested information regarding the draft Kootenai Subbasin Adaptive Management Plan being developed by the Tribe and requested that the draft document be provided.  The Tribe has loaded the working draft document onto the Tribe’s web site at http://www.restoringthekootenai.org/.

We were reluctant to provide this document at this time because this is a working document that is only partially complete and additional coordination and development of the document and associated processes still needs to occur.  This adaptive management plan is not a requirement of the NPCC program nor is it specifically required as a component of any of the Tribe’s projects, this is an initiative that the Tribe has undertaken in order to better manage their overall Fish and Wildlife Program. 

The purpose of the Kootenai Subbasin Adaptive Management Plan is to link each of the projects within the Tribe’s Fish and Wildlife Program via a subbasin scale framework in order to better understand and adaptively manage how those projects collectively contribute to ecosystem restoration in the Kootenai subbasin.  Once completed, the Kootenai Subbasin Adaptive Management Plan is intended to be a living document that will be refined and updated over time as new information becomes available, as results of previous restoration actions are realized, and as the Tribe’s Fish and Wildlife Program continues to mature. 

The Kootenai Subbasin Adaptive Management Plan is intended to provide a framework to formally integrate the Tribe’s various programs and projects.  However, it is important to understand that it is not intended to replace or supersede the specific, detailed monitoring and evaluation or adaptive management components of the individual projects that make up the Tribe’s Fish and Wildlife Program. 

The geographic scope of the adaptive management plan includes the Kootenai subbasin as measured from ridge top to ridge top.  Because this plan is designed to support the Tribe’s Fish and Wildlife Program projects, and because the Tribe has no authority to manage other agencies’ projects or programs, the administrative scope of the plan is limited to the Tribe’s Fish and Wildlife program projects.  However, in recognition of the size and geographic extent of the Kootenai subbasin, and cooperative efforts to manage fish and wildlife resources, data and analysis developed by other agencies will also be used to where possible provide critical supplementary information in support of this adaptive management plan.

The Tribe initially explored development of a program-scale adaptive management plan in 2004.  At that time the Tribe hosted a multi-agency adaptive management workshop designed to collect input from scientific experts and management stakeholders on development of a subbasin scale adaptive management plan.  Topics addressed in this workshop included: 1) identification of particular management options that have potential for restoring key functions in the Kootenai River ecosystem, and important attributes of these options, 2) evaluation of alternative plans for applying combinations of these options over the next few decades, and 3) review of key needs for improvement of monitoring programs in order to insure timely detection of intended immediate effects of each option as well as possible longer-term side effects.  The results of this workshop were recorded in 2005 in the document, Draft Kootenai River Adaptive Management Plan (Walters, Korman, Anders, Holderman, & Ireland, 2005).  For a variety of reasons, primarily related to work load on other projects, this effort was temporarily shelved. This initial document provided a general framework that helped guide the evolution of projects over time, particularly with respect to common ecosystem stressors and responses addressed by multiple projects. 

In 2010, with the completion of the Kootenai River Habitat Restoration Program and the general shift in emphasis of the Tribe’s Fish and Wildlife Program from assessment and evaluation to feasibility assessment and implementation, the Tribe reinitiated efforts to develop a subbasin-scale adaptive management plan in November 2010.  This effort has moved along in a start-and-stop fashion (interrupted by other program work, development of project proposals, etc.) and is currently on hold to be reinitiated in spring 2012. 

In the last review of the document internal Tribal team identified a number of missing items and areas of concern in the current draft document.  Future work sessions will occur in spring through fall of 2012 to: 1) identify and confirm program goals and objectives; 2) refine and finalize the list of metrics used in the program; 3) review and confirm protocols for data storage, confirm methods for data entry, validation, sharing and retrieval; 4) confirm details for coordination with critical non-Tribal entities (e.g., IDFG, BCMFLNRO, MFWP); and 5) develop the agenda and work plan for a fall 2012 meeting to review data from the 2012 field season and develop an initial set of adaptive management recommendations.  The results of this first meeting will be compiled and added to the current draft of the document.  A final review draft of the Kootenai Subbasin Adaptive Management Plan will be distributed prior to the Adaptive Management Team meeting in Fall 2012.  At the fall meeting, we will use the document as a guide for decision-making, and note any additional content that needs to be added so the document is an effective tool for guiding the adaptive management decision-making process.

In addition, the Tribe is in the process of identifying a team of external experts to assist in the review and refinement of the current draft document.  Completion of the final document is scheduled for January 31, 2013.

We hope the ISRP will recognize that this is a partial draft document and still very much a work in progress.  Toward this end, suggestions to improve the overall framework and content would be appreciated and will be incorporated into our future efforts to the extent possible. 

 

Additional Information in Response to ISRP Comments

The following additional responses address additional specific comments or questions identified by the ISRP that have not been otherwise addressed as part of the response to the ISRPs five specific requests.

1. Purpose: Significance to regional programs, technical background, and objectives

The ISRP reviewers noted that the proposal incorrectly stated that only the Kootenai River supports a naturally landlocked population of white sturgeon.  ISRP reviewers suggested that the Tribe review literature from the Nechako including McAdam et al. 2005 and McAdam et al. 2011.

We are embarrassed by the error in the proposal (which was replicated from an error in our Master Plan).  We have corrected the error in the Master Plan and the project proposal.  We are well aware of the Nechako population and the work of the Nechako sturgeon recovery initiative.  Steve McAdam is a member of the Upper Columbia White Sturgeon Recovery Initiative Technical Working Group which members or our team coordinate with regularly, and Steve also occasionally participates in Kootenai River White Sturgeon Recovery Team meetings.  Steve is also included on our technical review team for the project (CMART), although he has been on paternity leave for some time and has not been able to actively participate in recent reviews.  We are familiar with McAdam et al. 2005 and McAdam et al. 2011 and appreciative of the good work being done in the Nechako and the Upper Columbia for white sturgeon.

 

The ISRP reviewers commented that it would be helpful if the project objectives were more quantitative and included measures of incremental success.  The ISRP also suggested that objectives should include both habitat and demographic targets and be closely linked to the RME efforts. 

Please see response provided as part of our response to the ISRP request number 1.

 

The ISRP reviewers commented that project objectives appear to concentrate heavily on the focal species to the exclusion of others and that this approach is not ecosystem restoration.  The ISRP suggests there should be additional discussion of how the restoration actions will also benefit burbot, salmonids and other species such as cottids, which are not ESA listed or harvested but are important for trophodynamics and predation.

Please see the clarification in our response to the ISRP’s first request for response (i.e., provide more detail on feasibility assessment and design activities for Phase 2 and 3), regarding the selection and use of aquatic focal species.  We firmly believe that the KRHRP is an ecosystem-based restoration project.  The NPPC subbasin planning effort provided guidance about using focal fish species and the six focal species that were selected for analysis in the subbasin planning effort are often used by the Kootenai projects as “focal fish species”.  Additional discussion of the project benefits to burbot, salmonids and other focal species are included in the KRHRP Master Plan, specific examples of how we’ve integrated the needs of other focal species can be found in the Feasibility Assessment and Preliminary Design for the Phase 2 Upper Meander and North Side Channels projects (scheduled for implementation in 2012).  We have also provide additional specific information regarding habitat needs for burbot, bull trout and other salmonids in response to another ISRP comment under Project relationships, emerging limiting factors, and tailored questions for type of work 

We are also providing the following specific response regarding cottids.

Cottids feed on a range of prey items (Brusven and Rose 1981; Hershey 1985; McAdam 2011) and exhibit piscivory of other fish species’ eggs, larvae, and juveniles (Gadomski and Parsley 2005; McAdam 2011).  Cottids are themselves prey items for a number of other fish species.  Within the proposed project area, Cottids are common, but are spatially limited by suitable benthic habitat.  However, Cottids preferred habitat coincides with the preferred spawning substrate of several focal fish species.  This lends to Cottid success, as they find readily available food items within the benthic substrate in the form of benthic invertebrates and multiple life stages of fish. 

For the purposes of this project, this topic will focus on potential Cottid predation of larval sturgeon, burbot, and salmonids; as well as, the feedback loop of juvenile and adult burbot, salmonid and other native fish predation of Cottids.  Channel and substrate enhancements will likely benefit Cottids by increasing density and overall abundance.  This has negative and positive consequences.  A negative consequence may be increased predation of white sturgeon eggs and larvae (Miller and Beckman 1996; Gadomski and Parsley 2005; McAdam 2011).  Recent studies found that larval white sturgeon select coarse substrates with adequate interstitial spacing for cover immediately following hatch and during the passive/active transport stage that corresponds with the beginning of exogenous feeding in the water column (McAdam 2011).  Also, Gadomski and Parsley (2005) found that low turbidity, increased light, and lack of coarse substrate increased sculpin predation on white sturgeon larvae.  However, a positive consequence may be increased forage for burbot, bull trout, and westslope cutthroat trout.  With the reintroduction of burbot, and the potential increase of salmonid abundance, Cottid densities may be held in check; thus, reducing or minimizing any increased predation of larval sturgeon by restoring the natural checks-and-balances feedback loops in the proposed project areas.  Therefore, increased Cottid abundance may provide increased forage for burbot and salmonids without detrimental effects to larval sturgeon production.  Under natural conditions, the reproductive strategy evolved by sturgeon and most fish is to “predator-swamp” during early life stages.  However, given the reduced abundance of spawning white sturgeon in a given year, we agree this issue should be monitored long-term. 

Finally, without substrate enhancement in areas where sturgeons currently spawn, no larval recruitment will occur; therefore, a concern with Cottid predation is not relevant.  Additionally, without appropriate main-channel, side-channel, and littoral substrate/cover, early life stages of sturgeon will be suffocated, more easily predated, and will not find appropriate velocity barriers during their sequential passive/active transport phase. 

Again, the importance of coarse substrates with interstitial spaces to white sturgeon egg and larval survival is now documented.  However, the role of riparian/littoral habitat complexity in the early life development of Kootenai River sturgeon is less known.  Much of the Lower Kootenai River has been extensively altered for the past 100+ years.  These alterations have eliminated a vast amount of riparian and floodplain habitat.  Given the scientific communities’ acknowledgement regarding the importance of such habitats to entire ecosystems, it is highly likely restoration will benefit every species in the Lower Kootenai River in some manner ranging from biochemical processes to spur productivity to increased habitat complexity in order to support a balanced aquatic organism assemblage.  Tracking every hydrological, physical, and biological interaction is not feasible.  However, useful indicators of environmental conditions and biological trends are already incorporated into the Tribe’s biological monitoring associated with the conservation aquaculture program, the biomonitoring occurring under the nutrient addition project, and the IDFG monitoring efforts.  

 

2. History: Accomplishments, results, and adaptive management

The ISRP reviewers noted that the link to Kynard et al. 2010 could not be downloaded completely.

We have replaced the original link and the article should download fine now.  

 

The ISRP reviewers comment that several habitat projects have already been implemented on the Kootenai, but there is little evidence in the proposal that the response of the focal species to these projects has been assessed.

We assume the ISRP is referring to the pilot rock placement project near Shorty’s Island and the Phase 1a and 1b projects implemented under the Kootenai River Habitat Restoration Program in 2011.  The pilot rock placement project was intended only to test the feasibility of placing rock substrate on the clay riverbed.  The project funding was capped at $250,000, which was not sufficient to acquire and position the equipment that would have been necessary to place the rock in the river thalweg where the sturgeon spawning is occurring.  Moreover, the “rock” that was placed under this project was 6-foot boulder sizes and therefore not suitable to test the sustainability of interstitial spaces.  The hydrodynamics of the area where the rock is placed is not comparable to the conditions where the proposed substrate enhancement would occur.

Side channel pre-project monitoring was conducted for the Phase 1a and 1b projects prior to construction in the summer of 2011.  As-built monitoring was completed after construction. Winter monitoring is currently underway and additional side-channel monitoring will occur this spring/summer.  We plan to review and evaluate the initial results of the Phase 1a and 1b projects as part of the KRHRP monitoring and evaluation plan Core Manager Agency workshop in the fall of 2012.

 

The ISRP reviewers requested that the sponsor put the experimental fertilized egg and free-embryo releases in the context of the recent laboratory experiments reported by Kynard et al. (2010) and McAdam (2011).

In 2008, as a result of ongoing discussions within the Kootenai River White Sturgeon Recovery Team, members of the Recovery Team agreed to a five-year experimental release, from 2008 through 2012, of free embryos that were available in excess of annual production targets at the Kootenai Tribal hatchery.  The purpose of this effort was to test two hypotheses:

  1. Conditions at the release sites (gravel and cobble substrate, water column velocities at or in excess of 1 m/s) will allow for documentation of survival of early life stage Kootenai River white sturgeon;
  2. Kootenai River white sturgeon imprint on waters where they incubated and reared, and will return to these areas as adults (this would not be realized until 20 or more years until the fish reach sexual maturity and potentially return to natal release sites).  In addition to the preceding objectives, should released free embryos survive and recruit into the population, “take” (as defined under the Endangered Species Act) will have been reduced.

The results are expected to be helpful in designing remedies to restore and improve natural recruitment in Kootenai sturgeon, and may provide specific habitat and flow conditions for successful larval survival which may be applied to habitat improvement projects in the current spawning reach when considering microhabitat rehabilitation. This research may provide a means to evaluate the effectiveness of new approaches in the KRWS hatchery program to maximize production and genetic variability.   

To address recruitment failure, in 2008, IDFG and the Kootenai Tribe through a joint effort began releasing embryos (free embryos) at up to seven sites upstream from Bonners Ferry to determine drift and survival rates.  Embryos are hatched in the Tribal Hatchery facility and released at one to four days post-hatch over sites composed of gravel and cobble with water velocities typically exceeding 1 m/s.  All sites contain substrate and flow conditions that are similar to those used by successfully reproducing and recruiting white sturgeon populations in the Columbia basin (Parsley et al. 1993; USFWS 2006).  Long-term survival will be evaluated using gill nets when potential recruits become fully vulnerable to this gear type at least three years after release.  Although gill netting is the preferred method to evaluate the effectiveness of the free embryo releases in the long term, larval sampling with D-ring and ½ meter plankton nets directly below release sites has provided some information on drift and short-term survival.  Since free embryo releases began in 2008, larval sampling has been intermittent, with more effort being exerted when river conditions are optimal.  When flow and floating debris are manageable, larval sampling can and has yielded important results.  Over 3 million free embryos have been released into the Kootenai River form the KTOI conservation aquaculture program since 2008.  In 2008, one 14-day old sturgeon larva was collected in a side channel near Caboose Creek in the Canyon Reach near river kilometer 271. This capture was the first and only larvae sturgeon captured in plankton nets in the Kootenai River since monitoring efforts began in 1978. 

By-catch has varied as a function of effort and river conditions, but larval Catostomidae have been the most abundant fish larvae sampled in the nets each year (Rust and Wakkinen 2008, 2009, 2010).  Water temperature during the netting period generally ranged from 10 to 15°C.  In 2012, we plan to use the same release locations, and standard gill netting methods will continue to be used during subsequent years to assess recruitment resulting from these releases (sampling is performed by IDFG – Project 198806500).  Ultimately, program success will be realized when a significant brood year of unmarked juvenile sturgeon appears in our standard netting assessments.  Table 13 summarizes the chronology of release and hatchery-bound white sturgeon free embryos form 2008-2011.

Table 13. Chronology of released and hatchery-bound white sturgeon free embryo 2008-2011, Kootenai River.

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We agree with the ISRP regarding the critical importance of appropriate fine-scale substrate attributes (interstitial spaces) and flow field conditions for white sturgeon embryos free embryos and larvae.  We also agree that population-specific behaviors and substrate requirements are crucial, and dramatically regulate early life survival rates, and therefore the establishment and failure of year classes (see abstract from McAdam (2011) below).  Kynard et al. (2007, 2008, 2009, 2011) performed a series of informative laboratory habitat (substrate and velocity) choice experiments using various early life stages of Kootenai River white sturgeon, evaluated river conditions, that revealed similar population-specific suitability curves for various environmental metrics.  The relevant point for this response is that these issues are extremely important to the future of sturgeons in altered rivers, and to the design of habitat restoration actions in rivers, as indicated by McAdam (2011) and these studies by Kynard et al. (2007, 2008, 2009, 2011).  Project proponents are aware of these important issues and are incorporating them into design criteria for project restoration activities.

Abstract from McAdam 2011: To understand links between substrate and recruitment of white sturgeon (Acipenser transmontanus), I evaluated the effects of substrate condition on larval drift, hiding, and predation between hatch and 15 days posthatch (dph). Over porous substrates (small gravel = 1.2–1.9 cm; medium gravel = 2.5–5.0 cm; cobble = 10–15 cm), rapid interstitial hiding was observed from 0 to 6 dph at low water velocity (4 cm·s –1 ), whereas larvae drifted in response to nonporous substrates (sand < 0.2 cm; embedded cobble). Velocities of 20 cm·s –1 led to significantly lower drift only at 1 dph over small gravel. Hiding occurred an average of 2.0–13.3 s after release at 0–6 dph. Predation by sculpins (Cottus spp.) on larval sturgeon also decreased significantly in response to porous substrates at 1 dph. The strongest expression of increased hiding and decreased predation when small gravel was available suggests that yolksac larvae prefer small interstitial spaces created by that substrate. Considering behavioural responses in preferred natural spawning habitat suggests yolksac larvae predominantly hide in the vicinity of spawning locations. Identification of strong effects of substrate condition on age-specific drift and survival suggests that substrate degradation may contribute to recruitment limitations for sturgeon.

 

3. Project relationships, emerging limiting factors, and tailored questions for type of work

The ISRP reviewers commented that it is not clear that the information presented in the proposal supports the contention that the critical limiting factor for sturgeon habitat is the lack of appropriate spawning habitat, specifically, hard substrate on which fertilized eggs and attach.   Reviewers also comment that in regard to the discussion of a potential survival bottleneck during the early rearing period, no information is provided to verify that low productivity is the cause of this survival bottleneck.

We regret any confusion caused by our proposal content or omissions and provide the following information to help clarify what we do and don’t know about these topics.

Based on annual sampling, telemetry work, and analysis of data collected since 1990, two things have become invariably clear regarding ongoing natural recruitment failure for Kootenai River white sturgeon: 1) spawning occurs annually over an ~18 km reach from Shorty’s Island upstream to or slightly above Bonners Ferry; and 2) recruitment failure occurs during the embryo (incubation) stage prior to hatch.  Regarding this second point, spawning of white sturgeon in the Kootenai River from 1991–1998 has been confirmed by the collection of over 1,000 eggs or embryos using standard egg mat techniques; all efforts failed to collect any free embryos or other early life stages (Paragamian et al. 2001).  This trend has continued annually ever since sampling began in 1991 (Rust et al. 2010, 2011).

Kootenai sturgeon use atypical spawning habitat compared to other conspecific populations (Parsley et al. 1993; Anders 2002; Perrin et al. 2003; Nelson and McAdam 2012).  Kootenai sturgeon spawn in the upper meandering reach, which is characterized by low velocities, deposition of fine sediments, and bed materials including shifting sand dunes and intermittent exposed areas of lacusterine clay.  Exact spawning locations are inferred from egg and embryo collections.  During a recent 8-year study, only 15 white sturgeon eggs were collected over gravel and cobble substrates, while 1,193 eggs were collected over sand substrate (Paragamian and Kruse 2001).  The fine-sediment spawning substrate used by Kootenai River white sturgeon differs considerably from the gravel, cobble, boulder, and spawning substrates used by some other white sturgeon populations (Parsley et al. 1993; Anders 2002; Perrin et al. 2003; McAdam 2005).

Mortality of white sturgeon embryos, which are adhesive and demersal, may be due to suffocation (lack of gas exchange) from aggrading fine sediments in Kootenai River spawning areas, which are characterized by large mobile sand dunes on the river bottom, and possibly also to predation (Paragamian et al. 1998; Anders et al. 2002; Kock et al. 2006).  Current research and analysis by IDFG recently revealed a statistically greater median age of naturally produced embryos collected on gravel than silt/clay substrates (Pete Rust, IDFG, pers. comm).

This contention is further supported by empirical research addressing the sensitivity of incubating embryos to sediment exposure.  Replicated experimental exposure of Kootenai River white sturgeon embryos to Kootenai River sediment treatments significantly reduced mean embryo survival and mean length and weight of any surviving larvae (Kock et al. 2006).  Mean embryo survival was significantly (P=0.0001) reduced to 0-5% under sediment cover treatments of either 5 or 20 mm depths, compared to survival that exceeded 80% in the unexposed incubating controls (Kock et al. 2006) (mean embryo diameter was around 2 mm).  In a second experimental trial, embryo survival was significantly negatively correlated (P=0.001) with increasing duration of sediment cover; survival was significantly higher for embryos when covered for 4 days (d; 50% survival) or 7 d (30% survival) than for those covered for 9, 11, or 14 d (15-20% survival). Sediment cover also significantly delayed hatch timing (P=0.0001) and significantly decreased mean length of any surviving larvae (P=0.0001; Kock et al. 2006).

In summary, consistent results from more than 20 years of field sampling and data analyses regarding spawning areas, substrate conditions, bedload conditions and transport, inferred spawning locations, large embryo collections, failure to capture post-hatch life stages (free embryos or larvae), and the sensitivity of incubating embryos and early hatched larvae to sediment exposure collectively provide the supporting scientific basis for annual recruitment failure of the Kootenai River white sturgeon population occurring by the end of the embryo (incubating) stage.

A second potential survival bottleneck for natural production of Kootenai River white sturgeon has been suggested by Justice et al. (2009) based on reduced post-release survival rates of Age-0 hatchery produced fish during their first year at large (~15%) compared to an average post-release survival rate for Age-1 fish of ~60%.  Although authors of this paper suggest that this reduced survival rate of smaller, younger fish could be a negative density-dependent response, an alternative explanation suggests that reduced survival rate of Age-0 fish could simply represent lower survival rates associated with Age-0 vs. Age 1 fish.  This age-specific survival difference would be expected based on general population biology principles of fishes, given comparatively increased diet breadth (food availability), reduced limitation, and higher survival for larger, older fish (Age-0 vs. Age-1).  In addition to this age dependent function, this dichotomy could be further exacerbated by low productivity and limited food availability resulting from the cultural oligotrophication of the Kootenai River due to upstream impoundment and the loss of over 50,000 acres of historic floodplain (Daley et al. 1981; Ashley et al. 1999; Anders et al. 2002; Snyder and Minshall 2005; Schindler et al. 2011).  Furthermore, food availability could simultaneously be limiting to Age-0 but not Age-1 fish, due to differences in prey item selection of larval versus juvenile white sturgeon.

This observation of a possible second bottleneck for Age-0 fish was solely enabled by analysis of mark-recapture data from young juveniles produced in the Kootenai Tribe’s conservation aquaculture hatchery, since sufficient numbers of naturally produced fish of these ages to perform these types of analyses are unavailable.  Whether similar densities of naturally produced juveniles would exhibit the same responses remains unknown.

 

The ISRP reviewers state that many of the proposed habitat actions are focused more broadly on restoring the ecological health of the project reach rather than specifically addressing factors thought to impact sturgeon.  They comment that actions to restore bank stability, riparian vegetation, wetland habitat, etc. are all likely to make contributions to improved aquatic habitat, but it is difficult to determine whether or not these planned projects are in the most advantageous location to affect responses by the focal species.  They also suggest that additional information on the factors limiting the productivity of burbot and the various salmonid species that are intended to benefit from this project would have helped to verify that the proposed actions are located in an appropriate location.  

As explained in our response to the ISRP’s first response request (i.e., provide more detail on the feasibility assessment and design activities), the KRHRP is an ecosystem-based restoration project.  We are specifically seeking to restore habitat conditions that support all life stages of the six focal species identified in the KRHRP as well as other native fish populations.  We also described in that response how the restoration strategies, treatments and Phase 2 project locations were selected as part of the KRHRP Master Planning process and concept development for Phase 2.  If the reviewers look at our Draft Feasibility Assessment and Preliminary Design Document for the Phase 2 Upper Meander and North Side Channels projects (scheduled for implementation in 2012), this also provides a detailed example of how we are incorporating specific information about focal species habitat requirements, limiting factors and existing habitat conditions into our design process.

We are also providing the following information regarding burbot, bull trout and other salmonid species:

Burbot

Historically, burbot ranged throughout the project area.  Adult burbot were routinely caught in substantial numbers in the upper Meander and Braided Reaches and within spawning tributaries.  The most frequently fished area was Ambush Rock (RKM 244.5) the upriver extent of the Meander Reach as the river transitions from the Braided Reach.  Also, spearing and snagging of burbot in spawning tributaries was commonly practiced.  Since the 1960s and 1970s, burbot numbers have drastically declined to a status of functional extinction in the project area.  During 1979-1982, burbot fry and juveniles were still captured in low numbers within the ongoing and proposed habitat restoration areas and within several tributaries.  Subsequent efforts to capture early life stages in the Idaho portion of the Kootenai River have been fruitless.  However, routine agency sampling continues to capture a remnant of the population at Ambush Rock each winter.  Very small groups of adult burbot continue to congregate at Ambush Rock during the spawning season.  Although it is likely to some extent, it is not known if these adults are spawning in the vicinity of Ambush Rock or at upriver locations within the Braided Reaches.  Further, restoration of these reaches will support survival of hatchery-reared burbot.  When these fish attain sexual maturity within these and adjacent reaches, spawning within the Braided and Straight Reaches is likely.  Therefore, the series of pools and enhanced side channels will be very beneficial to burbot restoration efforts.

Limiting Factors

The Lower Kootenai River Subbasin stock is functionally extinct.  Therefore, a donor broodstock source(s) and an intensive aquaculture program are needed to restore this population.  Moyie Lake currently provides gametes to support objectives of Burbot Restoration Project. 

Libby Dam operations have caused unnaturally high and fluctuating late autumn, winter, and early spring hydrograph. The unnatural hydrograph has disrupted physiology and behavior, particularly in regards to reproductive physiology and behavior.

Libby Dam operations have caused unnaturally warmer thermograph during winter.  The unnatural hydrograph has disrupted physiology and behavior, particularly in regards to reproductive physiology and behavior.  Also, this is very important as temperature dictates egg development rate, and larval development and feeding schedules. 

Access to historical spawning tributaries is limiting.  Diking, agricultural practices, and lack of natural river geomorphological processes due to river regulation have greatly impacted the Lower Kootenai Tributaries.  Historically, geomorphological processes created alluvial fans at the mouths of tributaries.  However, this no longer occurs, and extensive sediment deposits have created almost un-passable barriers during low flows.  Historical accounts have documented the use of several tributaries as major spawning habitats.

Lack of quality spawning and rearing habitat in spawning tributaries is limiting.  Diking, agricultural practices, channel alterations, and lack of natural river geomorphological processes have greatly impacted the valley reaches of the Lower Kootenai Tributaries.  Historical accounts have documented the use of the valley reaches as major spawning habitats.  Most of the Lower Kootenai tributaries are high gradient, coldwater streams as they enter the river valley.  As slope diminishes, clean, coarse substrates are deposited while water temperatures remain cold.  Also, these reaches were naturally characterized by meandering channels and extensive riparian vegetation.  For almost every tributary, both characteristics no longer exist due to human activities.

Lack of quality spawning and rearing habitat in side-channels and main channel is limiting.  Diking, agricultural practices, channel alterations, and lack of natural river geomorphological processes have greatly impacted the Lower Kootenai main channel and side-channels.  Historical accounts have documented the use of side-channels and secondary floodplain channels across life history.

Loss of off-channel sloughs, secondary floodplain channels and backwaters have limited larval, juvenile, and adult rearing habitat and feeding areas.

Lack of general ecosystem function and elimination of floodplain productivity is limiting.  The Kootenai River no longer supports adequate zooplankton communities in terms of quantity and timing.  Larvae are particularly sensitive to environmental disruption as they require a live diet of zooplankton to survive a narrow window of opportunity before they reach a point of no return. A recent study of zooplankton in water bodies of Idaho and British Columbia that support burbot populations found that the Lower Kootenai River and a main burbot spawning tributary, Goat River, support low zooplankton densities (Hardy et al. 2008).  On a positive note, juvenile and adult burbot are diet generalists with a propensity for piscivory, and should benefit from recent nutrient addition, habitat restoration, and kokanee re-introductions.  Nutrient addition has increased the abundance and biomass of the native fish assemblage, and restoring kokanee provides additional forage for juveniles and adults within all habitats.  Juvenile and adult burbot will overlap with larval and juvenile kokanee in tributary, side-channel, and main channel habitats providing additional feeding opportunities. 

Habitat Requirements

Spawning: 

  • Flows typical of the natural hydrograph and thermograph.  In particular, natural winter spawning flows were typically the lowest of the annual hydrograph in combination with a descending thermograph leading to extremely low temperatures 1-2°C (Moyie Lake donor source spawns 1.0– 2.0°C).
  • A thermograph that gradually descends throughout Fall and Winter until water temperatures reach and are maintained at 1-2°C for several weeks to months is required to synchronize reproductive physiology and behavior.  Burbot spawn in groups of several to dozens of individuals per episode of gamete release.  Thus, reproductive synchrony is very important.
  • Coarse/clean substrate, variable depth 3-20 feet, low-medium velocity, and most likely areas of hyporheic upwelling. 
  • Burbot spawn in tributaries, side-channels, and littoral areas of rivers and lakes.  The donor stock from Moyie Lake selects littoral areas 3-20 feet deep with coarse substrate consisting of loose (unembeddded) large gravel, cobble, and some rubble to provide interstitial egg incubation and larval cover.  Also, visual observations noted that spawning areas appear to have secondary water circulation possibly caused by hyporheic upwelling.  This is known to be a variable important to spawning site selection by other demersal spawners.

Egg Incubation:

  • Temperature: 1-4°C.
  • Clean substrates free from fine sediments to avoid suffocation.

Larval Development:

  • Temperature: Below 5°C.  As water temperatures increase above 5-6°C, larvae suffer increased mortality.
  • Burbot larvae also require areas with habitat complexity for cover and resting.
  • Burbot larvae require low velocity habitat to feed.
  • Larvae are particularly sensitive to environmental disruption as they require a live diet of zooplankton to survive a narrow window of opportunity before they reach a point of no return.  Thus, unnaturally higher temperatures accelerate metabolism at the same time food is limited.  A recent study of zooplankton in water bodies of Idaho and British Columbia that support burbot populations found that the altered Lower Kootenai River and a main burbot spawning tributary, Goat River, support very low zooplankton densities.

Juvenile Development:

  • Temperature: below 16°C.  Unnaturally increased late summer and autumn temperatures affect survival and growth.  Temperatures above 16°C compromise survival of juvenile burbot.
  • Juveniles require a diverse diet of macro-invertebrates and forage fish species which are possibly limiting spatially and temporally due to the extensive habitat alterations.
  • Juveniles require habitat complexity as an ambush predator, and to avoid predation and cannibalism.

Adult Maturation:

  • Temperature: below 16 – 18°C.   Unnaturally increased late summer temperatures also affect survival and growth.  Temperatures above 20°C compromise growth and survival of adult burbot depending on sub-population adaptation, individual plasticity, and individual acclimation.
  • Temperature:  A natural thermograph with gradual seasonal changes during an annual cycle with temperatures ranging 1-18°C that supports the natural cycle of physiological processes of an aquatic poikilotherm. 
  • A natural hydrograph to support ecosystem function to provide food, cover, and migratory/reproductive cues.
  • Adequate food is an essential component of adult maturation.  On a positive note, juvenile and adult burbot are diet generalists with a propensity for piscivory, and should benefit from recent nutrient addition, habitat restoration, and kokanee re-introductions.  Nutrient addition has increased the abundance and biomass of the native fish assemblage, and restoring kokanee provides additional forage for juveniles and adults within all habitats.  Juvenile and adult burbot will overlap with larval and juvenile kokanee in tributary, side-channel, and main channel habitats providing additional feeding opportunities. 
  • Physical Habitat:  Adults are benthic dwellers and ambush predators.  Thus, benthic habitat complexity is beneficial.

The proposed KRHRP projects will support the biological objectives for burbot restoration, which include the following:

  • Restore consistent natural recruitment in at least three different spawning areas with a juvenile population of sufficient size to support the adult burbot population goal.
  • Establish a stable-sized population with sufficient age distributions to assure long-term population viability and persistence.
  • Produce and stock burbot at rates and frequencies to sustain a target population of 2,500 to 9,500 adults in the Kootenai River and South Arm of Kootenay Lake. 

Burbot should utilize the proposed habitat restoration areas to complete their life cycle or at minimum complete critical life history stages on a seasonal basis.   The proposed habitat restoration projects may provide the following for burbot, which are demersal by nature, and are demersal broadcast spawners:

  • Spawning adults – migratory cues and staging areas.
  • Gametes - microhabitat combinations for egg fertilization, dispersal, and deposition.
  • Egg Incubation – reduced sedimentation and imbeddedness with enhanced hyporheic flow.
  • Larval development – enhanced benthic substrate diversity providing interstitial microhabitat.
  • Current velocities and/or hyporheic flow to maintain benthic substrate or to assist egg incubation and larval dispersal.
  • Larval rearing – habitat diversity for feeding, resting, and predator/cannabalism avoidance.
  • Juveniles  – habitat diversity for feeding, resting, and predator/cannabalism avoidance.
  • Non-spawning adults – enhanced food web dynamics increasing food availability and feeding opportunities; enhanced channel structure to support positive bioenergetics.

The increased pool habitat along with the restored side-channels in the Braided and Upper Meander Reaches, and the restoration of tributary habitat and floodplain connectivity should support the biological objectives of restoring several spawning areas and providing optimal habitat combinations that supports all life stages of burbot.  Spawning adults typically rest in deep habitats, and then make a coordinated movement to congregate in tight groups (referred to as “spawning balls”) over shallower areas of 3-20 feet deep with reduced velocity, coarse substrate consisting of loose (unembeddded) large gravel, cobble, and some rubble to provide interstitial egg incubation and larval cover.  In similar fashion, non-spawning adults and juvenile burbot typically undertake nocturnal feeding excursions from deeper, slow-velocity resting areas into shallow, complex habitats with forage fish, crayfish, and aquatic invertebrates.  Thus, all life stages of burbot may utilize these reaches to a greater extent in the future due to increased prey availability and the increased habitat diversity to provide a range of optimal microhabitats.

Bull Trout

Bull trout (Salvelinus confluentus) are widely distributed through the lower Kootenai River, from Libby Dam downstream to Kootenay Lake in British Columbia, but do not appear to be abundant (KTOI and MFWP 2004).  Available data indicate that only several hundred adult bull trout occur in the entire core area downstream from Libby Dam, encompassing Kootenay Lake and the lower Kootenai River subbasin (KTOI and MFWP 2004).  Spawning and rearing by migratory adults occur in headwater tributaries draining portions of British Columbia, Idaho, and Montana.  Migratory adult and subadult bull trout forage and over-winter in Kootenay Lake and the Kootenai River.  Adult bull trout are known to migrate downstream from Kootenai Falls, and a few have been observed to migrate back upstream past the falls (KTOI and MFWP 2004).  Bull trout spawning in the mainstem Kootenai River has not been documented and spawning probably does not occur (and didn’t occur historically) due to lack of suitable habitat and water temperatures outside the suitable spawning and incubation ranges (USFWS 2002). 

Bull trout limiting factors can be described in terms of their Endangered Species Act designated critical habitat primary constituent elements (PCEs) and the current status of the environmental baseline of the mainstem Kootenai River.  The environmental baseline includes the past and present impacts of all federal, state, or private actions and other human activities.  Biological requirements can be characterized in terms of a properly functioning condition (PFC) concept.  PFC is the sustained presence of natural habitat-forming processes in a watershed (e.g., riparian community succession, bedload transport, precipitation runoff pattern, channel migration, productivity) that are necessary for the long-term survival of the species through the full range of environmental variation.  PFC, then, constitutes the habitat component of a species’ biological requirements.  The indicators of PFC vary between different landscapes based on unique physiographic and geologic features.  For example, aquatic habitats on timberlands in glacial mountain valleys are controlled by natural processes operating at different scales and rates than are habitats on low-elevation coastal rivers or arid desert river systems.  The PFC concept includes a recognition that natural patterns of habitat disturbance will continue to occur.  For example, floods, landslides, wind damage, and wildfires result in spatial and temporal variability in habitat characteristics, as will anthropogenic perturbations. 

The existing environmental baseline of the mainstem Kootenai River is summarized below in terms of habitat conditions that are important to sustain the long-term persistence of bull trout foraging, migration, and over-wintering (FMO) habitat in the mainstem Kootenai River.  Appropriate habitat conditions are defined by critical habitat PCEs.  Bull trout limiting factors are summarized by the degree to which the environmental baseline in the mainstem Kootenai River supports critical habitat elements.  PCE conditions are rated as “properly functioning (PFC)”, “impaired (IC)”, or “not properly functioning (NPF)”.  A summary of each PCE element follows Table 14, along with a justification for the status of each PCE element in the mainstem Kootenai River.  PCEs rated as NPF would be considered primary limiting factors of bull trout use of the mainstem Kootenai River.  PCEs rated IC may also be important limiting factors.

Table 14.  Environmental baseline summary of relevant bull trout critical habitat PCEs in the Kootenai River (limiting factors analysis).

PCE

Function

Description of PCE

Cause of Degradation from PFC

PCE – 1 Cold Water Springs, Seeps, and Hyporheic Flows

NPF

The Kootenai River has been largely disconnected from its floodplain; riparian vegetation has been largely degraded; no known significant cold water springs or seeps are known to occur.

Libby Dam operations, diking, and floodplain development have likely altered the hyporheic flow regime.

PCE – 2 Migratory Corridor

PFC

While the habitat in Kootenai River has been highly modified compared to historical conditions, there is no known impediment that would hinder migratory bull trout movement through the reach during the probable migration time.

NA

PCE – 3 Forage Base

IC

While specific abundance of all potential forage species is unknown, it is likely that the large degree of habitat modification of the Kootenai River has reduced the abundance of forage species.

Libby Dam operations, as well as riparian and floodplain alterations, have reduced habitat complexity, likely reducing productivity of forage fish and aquatic invertebrates.

PCE – 4 Habitat Complexity

NPF

Kootenai River banks are highly actively eroding in many areas, large woody debris is scarce, and pool forming processes have been hindered.

Libby Dam operations, as well as riparian and floodplain alterations, have reduced habitat complexity,

PCE – 5 Water Temperature

PFC

Temperatures during the likely time migratory bull trout inhabit the Kootenai Reach (most likely in post-spawn late fall through winter to mid-summer, are on average between 2 to 15°C (i.e., less than 60°F).

Libby Dam operations have altered water temperatures, resulting in cooler temperatures in the early summer. 

PCE – 6 Spawning Substrate

NA

Spawning is not suspected currently or historically in the mainstem Kootenai River.

NA

PCE – 7 Seasonal Hydrograph

IC

Seasonal hydrograph patterns are similar to historic conditions, although peak flow magnitude has been reduced.

Libby Dam operations have reduced the peak flow magnitude.

PCE – 8 Water Quantity and Quality

IC

Water quality is generally good, but peak flows have been reduced.

Libby Dam operations have reduced the peak flow magnitude.

PCE – 9 Non-native Species

IC

Several non-native species are present that could compete or prey on migratory subadult and adult bull trout, although the specific abundance of non-native species is unknown.  If abundance of non-native fish is high, this PCE may be NPF.

Illegal and legal stocking has occurred.

Notes: NA = Not Applicable, PFC = Properly Functioning Condition, IC = Impaired Condition, NPF = Not Properly Functioning

Desired habitat conditions for bull trout in the mainstem Kootenai River are defined by the Endangered Species Act listing of critical habitat critical habitat primary constituent elements (PCEs) related to foraging, migration, and over wintering (FMO) habitat uses for migratory adult and sub-adult bull trout.  Relevant bull trout critical habitat PCEs to the mainstem Kootenai River include:

  • PCE 1: Springs, seeps, groundwater sources, and subsurface water connectivity (hyporheic flows) to contribute to water quality and quantity and provide thermal refugia.
  • PCE 2: Migratory habitats with minimal physical, biological, or water quality impediments between spawning, rearing, overwintering, and freshwater and marine foraging habitats, including but not limited to permanent, partial, intermittent, or seasonal barriers.
  • PCE 3: An abundant food base, including terrestrial organisms of riparian origin, aquatic macroinvertebrates, and forage fish.
  • PCE 4: Complex river, stream, lake, reservoir, and marine shoreline aquatic environments, and processes that establish and maintain these aquatic environments, with features such as large wood, side channels, pools, undercut banks and unembedded substrates, to provide a variety of depths, gradients, velocities, and structure.
  • PCE 5: Water temperatures ranging from 2 to 15 °C (36 to 59 °F), with adequate thermal refugia available for temperatures at the upper elevation end of this range.  Specific temperatures within this range will depend on bull trout life-history stage and form; geography; elevation; diurnal and seasonal variation; shading, such as that provided by riparian habitat; streamflow; and local groundwater influence.
  • PCE 7: A natural hydrograph, including peak, high, low, and base flows within historic and seasonal ranges or, if flows are controlled, minimal flow departure from a natural hydrograph.
  • PCE 8: Sufficient water quality and quantity such that normal reproduction, growth, and survival are not inhibited.
  • PCE 9: Sufficiently low levels of occurrence of nonnative predatory (e.g., lake trout, walleye, northern pike, smallmouth bass); interbreeding (e.g., brook trout); or competing (e.g., brown trout) species that, if present, are adequately temporally and spatially isolated from bull trout.

While the descriptions of critical habitat PCEs would suggest habitat requirements of bull trout are known, in actuality, very little peer-reviewed literature has quantified habitat requirements for bull trout FMO uses.  Further discussion regarding migratory adult and subadult bull trout FMO habitat requirements follows.

Habitat components that have been associated with bull trout include cool water temperature, high degree of instream cover, complex and stable channel form, clean and unembedded spawning and rearing substrate, and unobstructed migratory corridors (Howell and Buchanan 1992; Rieman and McIntyre 1993).  Water temperature above 15°C (59°F) is believed to generally limit bull trout distribution, although migratory bull trout have been documented in migratory corridors with temperatures well over 16°C for varying time periods (Howell et al. 2009, Goetz et al. 2004, Baxter 2002, Dunham et al. 2003).  While it is thought that a high degree of habitat complexity, such as abundant pools and large woody debris, is associated with bull trout presence, these attributes represent optimal conditions as described in the scientific literature that are correlated with headwater resident adult bull trout, migratory bull trout during spawning, and early rearing life stages.  These habitat associations are not necessarily valid for large migratory adult and subadult bull trout that are over-wintering in large mainstem river reaches, such as the lower Kootenai River. 

Other than an abundant forage base, unobstructed upstream and downstream passage conditions, and water temperatures generally below 15°C, little is known about FMO habitat requirements for migratory adult and subadult bull trout, especially in large river reaches such as the lower Kootenai River.  The most recent comprehensive review of published peer-reviewed scientific literature on bull trout habitat use (24 articles reviewed) only found two articles addressing bull trout over-wintering and foraging habitat quantification in large mainstem rivers[1] (Al-Chokhachy et al. 2010).  Al-Chokhachy et al. (2010) identified “the need for elucidation of habitat use patterns in downstream reaches, which may act as critical overwintering habitat or migratory corridors”.  The only peer-reviewed published studies on subadult habitat use on the Flathead River may not be applicable to the Kootenai River.  Overwintering conditions are harsh in the upper Flathead River system due to anchor and frazil ice formation (Muhlfeld and Marotz 2005).  Deep, slow habitats used by subadult bull trout in the Flathead River likely provide areas of protection from these unfavorable conditions, which may not be of concern on the Kootenai River where anchor and frazzle ice are not a common issue.  Lowery’s 2009 unpublished data indicate that on the Skagit River, where anchor and frazzle ice are not a concern, subadult bull trout commonly use shallower river margin habitat in winter, and were essentially absent from the deepest pools in that study reach.

Although the scientific literature is largely lacking in habitat quantification of adult and subadult bull trout FMO habitat types, it is apparent that bull trout can successfully use a wide variety of habitats, such as lakes and reservoirs (Ratliff et al. 1996); large mainstem river reaches (Baxter 2002); estuarine river reaches, bays, and marine beaches; (Goetz et al. 2004), and the ocean (Brenkman and Corbett 2005).  The commonality in these habitat types is not a certain set of physical parameters specific to bull trout, but rather the presence of forage species, as migratory adult and subadult bull trout are known to be highly piscivorous.  Lowery (2009) reported that adult and subadult bull trout preyed heavily on fish eggs (salmon and sucker) and resident fish species (primarily cottids, dace, and whitefish), and seasonally on juvenile trout (rainbow/ steelhead smolts).  Goetz et al. (2004) reported that anadromous bull trout prey heavily on surf smelt, cottids, and sand lance in marine and estuarine areas.  In lakes and reservoirs bull trout are known to prey heavily on kokanee and whitefish (Beauchamp and Van Tassell 2001).  Large migratory bull trout in low productivity fluvial systems and can even impose a self limiting population control through heavy cannibalism of juvenile bull trout when a lack of other prey species occurs (Shappart unpublished data/observations on Mill Creek, WA and OR).

What is clear is that migratory bull trout using the mainstem Kootenai River require an abundant forage base.  An abundant forage base in a large river is driven by primary productivity.  The Kootenai River is channelized and largely disconnected from its floodplain.  Without marine derived nutrients from anadromous fish (due to downstream migration barriers, both anthropogenic and natural), Kootenai River primary productivity is even more dependent on riparian and floodplain nutrient inputs.  Floodplain and riparian productivity, and complex side channel habitats have been shown in many studies to be important for macroinvertebrate and juvenile fish production, which intern provides forage for all fish, including bull trout.  Therefore, restoration of riparian floodplain connection and riparian condition is a key component of the Kootenai River Habitat Restoration Program, which address bull trout critical habitat PCE No. 3 (abundant forage base) and PCE No. 4 (habitat complexity). 

Reconnection of floodplains can also enhance hyporheic and surface water flow interactions addressing PCE No. 1, and in combination with riparian vegetation restoration can influence water temperature, addressing PCE No. 5.  Providing riparian restoration and vegetated buffers between active agricultural production can improve water quality, addressing PCE No. 8.

Bull trout are thought to have more narrow habitat requirements than other salmonids, such as cutthroat and rainbow trout, and whitefish.  Addressing bull trout critical habitat PCEs should also improve habitat conditions for these species in the mainstem Kootenai River as well, as these entire habitat attributes are also important for these salmonids.

Other Salmonids

Other salmonid species are known to be present year-round within the mainstem Kootenai River.  IDFG has monitored fish species abundance and biomass annually as part of the Kootenai Tribe/IDFG project 199404900.  The following species have been collected and monitored since 2002, and are listed in order of highest abundance to lowest abundance in number of individuals.

  • Mountain Whitefish Prosopium williamsoni
  • Rainbow/Redband Trout Onchorhynchus mykiss
  • Westslope Cutthroat Trout Onchorhynchus clarki lewisi

Kokanee (Onchorhynchus nerka) juveniles and adults are also found in the mainstem Kootenai River during downstream emigration after entrainment through Libby Dam or during spawning migrations toward the Canyon Reach.  Limiting factors for each of these species are described below.

Columbia River redband trout and westslope cutthroat trout populations have been impacted by degraded riparian condition, fine sediment, high water temperatures, and channel instability in tributary habitat to the Kootenai River (KTOI and MFWP 2004).  In the mainstem Kootenai River, limiting factors include altered hydrograph and thermograph due to Libby Dam, degraded riparian condition, and fine sediment.  Fish passage barriers that restrict trout spawning migrations are also considered to be a limiting factor.  Hybridization with non-native coastal rainbow trout is also a concern.  Whitefish limiting factors are likely similar to those for trout in the mainstem Kootenai River.

There appears to be a relatively consistent ontogenetic habitat shift by salmonids as they grow from age-0 through adults. Age-0 salmonids use relatively slow and shallow water habitats commonly found along river and stream margins. As young salmonids grow they move into progressively faster and deeper water, but they take advantage of velocity breaks by using shear velocities where fast and slow water habitats are located in close proximity to each other. By locating themselves in relatively slow water close to much faster water they take advantage of fast water delivering food items, while conserving energy by holding in slower water and making short forays into the fast water to feed.  Water depth and physical cover are important for protection from predators.

Side channels of rivers appear to provide important habitats, especially for juvenile salmonids (both trout and whitefish).  Even seasonally ephemeral side channels appear to provide important juvenile salmonid habitats. Most research suggests that wide daily fluctuations in river flows are likely detrimental to growth and survival of salmonids, especially for incubating embryos and juvenile salmonids. Complex habitats in the form of interstitial spaces within the substrate or along riprap banks, off-channel habitats (side channels, backwaters, and ponds), organic debris (wood), diverse and moderately dense streamside vegetation, and pool habitats appear important for maintaining robust salmonid populations.

Pools are very important to larger juvenile and adult salmonids and may allow fish to survive in side channels that are subjected to periodic dewatering. Pools and interstitial spaces within the stream or river beds are critically important winter habitats.

Westslope cutthroat and redband trout feed primarily on macroinvertebrates, particularly immature and mature forms of aquatic insects, terrestrial insects, and, in lakes, zooplankton.  These preferences for macroinvertebrates occur at all ages in both streams and lakes.  Whitefish have a similar diet.  All three species rarely feed on other fish.

It is generally understood that kokanee fry move immediately to open waters after emergence from spawning areas, whether from tributaries or beach spawning sites.  Once in the limnetic area, feed primarily on zooplankton, especially copepods and cladocerans (KTOI and MFWP 2004).  The West Arm of Kootenay Lake kokanee behave differently than most studied kokanee populations.  Fry move from the natal streams and associate themselves with the shoreline for the first two months before moving to open water within the West Arm (KTOI and MFWP 2004).  Benthic organisms, aquatic insects and littoral zooplankton are consumed in addition to pelagic zooplankton. As the summer advances, fry move off shore and utilize macrozooplanktors and mysids (KTOI and MFWP 2004).

As described for bull trout, floodplain reconnection, riparian enhancement, and side channel restoration projects will increase productivity and habitat complexity that will benefit westslope cutthroat, redband trout, and whitefish.  In addition, productivity improvement will benefit the Kokanee forage base. 

The ISRP reviewers also note that the effect of non-native species, especially brown trout and Didymo deserve additional consideration.

Didymo – As indicated in our proposal, the Tribe and local partners are aware of the presence of Didymosphenia geminata (Didymo) in the Kootenai River.  We are actively coordinating with the various agencies and entities involved with current and proposed Didymo research and monitoring in the Kootenai River.  

Dense Didymo mats have been observed and monitored during recent years in the river immediately downstream from Libby Dam (Greg Hoffman, USACE Libby Dam, pers. comm.) and we are aware of the potential ecological concerns regarding downstream transport of this invasive diatom.  Although Didymo cells continue to be identified in samples collected by the Tribe’s Ecosystem Restoration project biomonitoring program (199404900), no evidence of invasive Didymo blooms downstream from Kootenai Falls in Montana has been observed to date.

However, to address this threat and the need to better understand the distribution and ecology of D. geminata in the Kootenai River, personnel from the U.S. Army Corps of Engineers (Greg Hoffman), MFWP (Ryan Sylvester, Jim Dunnigan), the Kootenai Tribe (Genny Hoyle), the South Dakota School of Mines and Technology (Dr. P.V. Sundareshwar), USGS and the University of Colorado (Sarah Spalding), the University of Idaho and Cramer Fish Sciences (Drs. Frank Wilhelm, Paul Anders), and others are collaborating on several complementary research and monitoring projects in the Kootenai River.  Additional world Didymo experts (Drs. Max Bothwell (UBC) and Cathy Kilroy, NIWA, New Zealand) are providing input and guidance on many aspects of these studies and monitoring programs.

The U.S. Army Corps of Engineers has secured funding for the construction and operation of two portable mesocosms (16 replicated troughs each) to study the effects of chemical and environmental conditions on Didymo growth and colonization at the tailrace of Libby Dam. MFWS will continue to monitor and evaluate the status of Didymo in the Montana section of the river immediately downstream from Libby Dam.  MFWP also recently secured funding for a 3-year Ph.D. project to study the effects of various chemical and environmental conditions of Didymo growth on site in Montana in mesocosm systems under the guidance and supervision of limnologist Dr. Frank Wilhelm (University of Idaho).  Cramer Fish Sciences was also recently awarded a small grant from the USFWS to develop and implement a program to extend coordinated Didymo monitoring further downstream into Idaho to monitor potential downstream range expansion. 

Partners in the Kootenai River are working cooperatively to assess the current status and identify future trends of Didymo in the Kootenai River, while advancing our knowledge of Didymo biology, ecology, and management options for this invasive diatom.

Brown trout – A total of 21 non-native brown trout have been sampled from five sites in the Kootenai River from 2003 through 2010 from a total of five sites over a 54 km reach.  This reach extends from rkm 285.6 in the lower Montana section downstream to the upper Meander Reach at Shorty’s Island in Idaho (rkm 231.4; IDFG unpublished data) (Table 15 and Figure 11).

Table 15.  Kootenai River brown trout sampling results 2002 through 2010. 

Year

# Brown trout sampled

Site

River km

River Reach

State

2002

1

KR6

250.0

Braided

ID

2003

0

-

-

-

-

2004

0

-

-

-

-

2005

1

KR10

285.6

Canyon

MT

2006

2

KR6

250.0

Braided

ID

1

KR10

285.6

Canyon

MT

2007

2

KR6

250.0

Braided

ID

2

KR9

262.2

Canyon

ID

4

KR10

285.6

Canyon

MT

2008

2

KR6

250.0

Braided

ID

3

KR10

285.6

Canyon

MT

2009

1

KR9.1

276.1

Canyon

ID

2010

1

KR4

231.4

Meander

ID

1

KR9.1

276.1

Canyon

ID

Of the 21 brown trout collected during this period, 12 were collected in Idaho and 9 were collected in Montana.  In Idaho, 1 was collected in the Meander Reach, compared to 7 and 4 from the Braided and Canyon reaches respectively.  From 0 to 8 brown trout were caught annually, with the highest annual catches during 2007 and 2008, at 8 and 5 fish respectively. 

image026

Figure 11.  Number of brown trout collected in the Kootenai River 2002 through 2010.

While the number and catch rates of brown trout are quite low, the Tribe and the IDFG are monitoring, and will continue to monitor, these trends and potential threat of deleterious effects associated with this non-native species.  No brown trout were collected during these years at the upstream unimpounded site at Wardner BC, upstream from Libby Reservoir (rkm 445.0).  An additional 4 brown trout were collected from annual fish sampling in 2011 that are not accounted for in the previous discussion (C. Gidley, IDFG, pers. comm. 2012).

4. Deliverables, work elements, metrics, and methods

The ISRP reviewers comment that it is difficult to understand how accurate estimates of project costs could be generated prior to the completion of he feasibility assessment and project design.

The larger context for the response to this question (i.e., detail on the feasibility analysis and design process) is provided in the response to the ISRPs first requested response.  Following is additional detail regarding development of cost estimates.

The design development, and associated cost estimating process, involves professional construction estimators, project managers and engineers all of whom are familiar with projects of this nature and size and specifically familiar with the Kootenai River.  The means and methods being utilized for the design development and cost estimation for the KRHRP are not unique to this project.  The Tribe is using standard, tested and accepted industry practices for developing projects of this type (habitat and river restoration) and size.  Construction costs estimates are developed and then refined at the concept, preliminary and final design stages.

Depending on the specific project, types of construction risks, challenges involved and the amount of unknown issues that are generally reduced during later design stages, contingencies are used in the cost estimates.  This is to ensure, that relative to the design stage, the cost estimate reflects the risks (unknowns) related to construction.

The KRHRP Master Plan provided estimated construction costs (Chapter 7) associated with the each of the habitat treatments and scaled approaches identified in the Master Plan.

In general, certainty around cost estimates depends on being able to break apart and define an organized scope of work and materials to the smallest level of detail, and then to break down direct and indirect costs associated with each detail.  Even in the early planning stages where work and deliverables may not be well defined, a formal and systematic approach can be followed to define work to the most accurate level possible.  The system of organizing a scope of work into components to which costs can be applied is called a “Work Breakdown Structure” This methodology is the basis for all standardized computer-based construction cost estimating programs utilized by cost estimators for projects of this nature and most any other large construction project.

To develop construction cost estimates for the KRHRP projects the Tribe contracted with a construction firm with extensive experience planning, estimating, and building projects of similar scope and scale.  Representatives from this firm teamed with the Tribe’s project planning and engineering design contractors on a number of occasions to review the proposed restoration projects.  They also visited the project area in order to view specific on-the-ground conditions and develop a more thorough understanding of the proposed types of projects.  Based on this information, at the concept stage (Master Plan) the construction firm provided estimated construction and construction related (indirect) costs for the scenarios presented in in the plan for each of the project reaches (i.e. Braided Reaches 1 and 2, Straight Reach and Meander Reaches 1 and 2).

The conceptual costs for the implementation scenarios for each project reach were then translated into unit costs (e.g. linear feet, cubic yards of cut, cubic yards of fill, acres, etc.) in order to provide a flexible and relatively accurate way to gauge potential project costs by reach, scenario and treatment.  This approach to development of unit costs based on actual construction estimates by reach and implementation scenario provided a conceptual framework for ensuring initial identification of potential constraints, means and methods, estimates of economies of scale, and costs specific to the regional location of the project were considered (as opposed to applying gross unit figures from a similar project in a different locale and scaling up or down).  The cost estimates presented in the Master Plan included direct and indirect costs for all cost categories.

Using the actual costs from the Phase 1 project implementation, the Tribe’s cost estimator and engineers reviewed the accuracy of the Phase 1 concept and preliminary design cost estimates against the cost estimates presented in the Master Plan.  The concept level cost estimates were largely accurate, but where necessary adjustments were made to reflect the more refined costs associated with the 2011 implementation.  Using the concept designs for the Phase 2 projects the team translated the concept designs into updated unit costs and then rolled these up.  These estimates are then adjusted for inflation based on a range of potential targeted implementation dates and include contingencies to account for the variance between concept and preliminary design. 

A potential large cost variable in habitat projects of the sort proposed in the KRHRP, and thus a source of uncertainty, are materials.  In the case of the KRHRP specifically, wood and rock, which depending on the project can be around 30 to 70% off the total cost.  This issue was effectively addressed in the Phase 1 projects through use of a local contractor who was able to secure wood for the project at considerably lower cost than had initially been estimated at the concept level.  The Tribe is working with this contractor to identify sources of wood and rock materials for the Phase 2 projects.  The Tribe is also working with BPA to develop contract mechanisms to facilitate securing stable supplies of rock and wood for the project.

We have a high level of confidence in the conceptual cost estimates provided for the Phase 2 projects.  These estimates will be updated and refined at the preliminary and final design stage. 

 

The ISRP reviewers requested clarification on several topics related to the Shorty’s Island/Meander Reach substrate augmentation project:  

  • It would be helpful to obtain information on how impacts to the existing spawning substrate will be avoided during the execution of construction for this project. 

Kootenai sturgeon are currently spawning over bed materials composed of shifting sand dunes and intermittent exposed areas of lacustrine clay in the Shorty’s Island/Meander reach project area.  There is essentially no suitable substrate in this area; thus the need for the substrate augmentation project.  Due to the lack of substrate to impact, there are no anticipated impacts to avoid. 

  • It would be useful to obtain further information on how reliable the models are that were used in developing this design.

Two models were used to develop the design for the Shorty’s Island substrate augmentation project in the Meander Reach.  A one-dimensional USACE HEC-RAS model was used to estimate existing and proposed conditions hydraulics including depth, velocity and water surface elevations.  A two-dimensional USGS FaSTMECH model was used to evaluate more specific hydraulic conditions in the area of the proposed substrate placement and to identify potential influences of the substrate placement on local hydraulic conditions.  The models were calibrated using measured water surface elevation data from nearby USGS real time gauges and supplemented with data from a network of stage recorders.  Riverbed bathymetry was surveyed using a multibeam echosounder.  As such, we feel that reliability of both models is high.

Interpretation of model hydraulics and prediction of the effects of hydraulics on sediment transport characteristics are less reliable and require professional judgment from experienced river science experts.  The Kootenai Tribe and U.S. Army Corps of Engineers co-hosted a technical modeling workshop in early February 2011 in Seattle, WA to address questions related to modeling interpretation and specifically, to look at questions related to the sustainability of the substrate enhancement project as presented in the 35% design.  The group reviewed a number of design and modeling questions but in particular they were tasked with determining whether: 1) the surfaces of the substrate augmentation be covered with silt or sand (which would make it difficult for eggs to adhere), 2) the necessary thickness of the substrate mats from an engineering and sustainability perspective (they were initially designed as 8-foot thick mats which would be expensive from a construction perspective and might have implications to hydraulics in the spawning area), and 3) whether the interstitial spaces in the substrate mats would become embedded or would remain largely clear (which is critical for providing larval hiding spaces as well as additional areas where eggs might settle).  The objective of the workshop was to identify areas of agreement and identify areas where additional feasibility analysis might be required.  This information will in turn be provided to the co-managers and other technical experts to help inform additional design and scoping work on the project.  The outcome of the workshop based on analysis of current modeling indicated 1) consensus agreement that the surface of the substrate would remain clear of silt or sand and eggs would be able to adhese, 2) consensus agreement that the substrate beds only need to be 2 feet thick to function as intended and not be inundated by sand dunes in the reach, 3) and a range of views and remaining uncertainty regarding the question of sediment gradually infilling the interstitial spaces in the substrate mats.  Workshop participants identified several potential analyses that could be undertaken to improve confidence in substrate sustainability.  Once this work has been accomplished a revised modeling recommendation will be completed and the preliminary designs revised accordingly.  

  • The proposal indicates that the development and calibration model being used to support the engineering designs for the substrate placement at Shorty’s Reach is only 23% complete. Is it premature to rely on this tool for the design of a major engineering project?

We are not sure what the source of this information is; it may have come from an error or typo in a document.  As stated previously, we have a high level of confidence in the models being used, and more importantly in the level of expertise we have on our team to be able to interpret those models.  

 

The ISRP reviewers comment that it is not clear why so much emphasis is placed on riparian habitat when the benefits of riparian conditions to sturgeon rearing has been questioned (McAdam et al. 2005).  They add that if the riparian components of the project are intended to primarily benefit species other than sturgeon, this fact should have been discussed in the proposal.

As explained in the response to the ISRP’s first comment (response to request for more detail on the feasibility assessment and design activities for Phase 2 and 3 projects), six focal species are identified in the KRHRP.  The second project objective specifically identifies restoration of habitat conditions that support all life stages of burbot, bull trout, kokanee, redband and westslope cutthroat trout. 

The ISRP reviewers are correct in noting that this project incorporates a significant amount of riparian habitat and off-channel reconnection work.  The KRHRP project was initially an offshoot of the Tribe’s conservation aquaculture project (198806400), and a response to the fact that hatcheries cannot and should not be expected to restore altered physical habitat conditions.  The Tribe also realized early on that failure to address suspected post-development physical habitat limitations could significantly undermine the success of its conservation hatchery program. 

The KRHRP project is designed to provide survival and recruitment benefits to sturgeon both directly (by addressing migratory, spawning and rearing habitat and food availability limitations) and indirectly (by providing habitat diversity and opportunities for off-channel primary and secondary production and food web complexity required to support sturgeon and other fish and invertebrate assemblages).

The approach of the KRHRP project is consistent with the Tribe’s holistic view embodied in the development, implementation, and coordination of its BPA-funded physical habitat (200200200), population viability (198806400), and nutrient-based (199404900) restoration projects.  We recognize the need to simultaneously and successfully address three essential pillars of ecosystem restoration: 1) physical habitat restoration, 2) the provision of demographically and genetically viable fish populations to found future generations, and 3) restoration of an adequate nutrient supply to support all needed biological processes. The failure to successfully mitigate any one of these three pillars would be expected to significantly jeopardize the success of any other restoration and recovery activities in the post-development Kootenai River ecosystem.

Given the importance of the flood-pulse (Junk et al. 1989) and serial discontinuity (Ward and Stanford 1983) concepts of large river-floodplain ecology, along with recent derivations and developments such the river machine model (Nester et al. 2011) to successful restoration of the Kootenai River habitats, the Tribe and co-manager believe that the importance of the physical habitat improvement measures proposed by this project cannot be underestimated.  

Thus, proposed restoration actions represent an irreplaceable component of the nutrient-habitat-population interface being collectively addressed by the suite of ongoing Kootenai Tribe projects.  From a broader ecological perspective, empirical research on many aspects of the post-development biological communities and physical habitat issues in the Kootenai River confirms the existence of an over-arching suite of limiting factors that collectively restrain recovery of individual populations and entire biological communities. This project addresses the physical habitat linkages to these limitations.

As stated in our response to ISRP Comment #2(a) from the Kootenai Tribe’s project 199404900, the Tribe understands the multi-dimensional nature of ecological processes, and by association, of ecosystem restoration.  Based on this recognition, project proponents have developed, implemented, and continue to propose a coordinated array of physical habitat, nutrient, and interim (hatchery) fish population restoration projects designed to restore the Kootenai River’s biological productivity and ecological functions.

As a prominent post-development feature particularly relevant to this project, the river has lost over 50,000 acres of its natural floodplain and the associated flood pulse over the past 100 years, which historically drove biological productivity and habitat diversity in this large river-floodplain ecosystem (Northcote 1973; Anders et al. 2002).  The Tribe’s conservation hatchery program is currently operating as an interim life support system for Kootenai sturgeon and burbot, that without intervention would be extinct prior to completion of the physical habitat restoration needed to restore natural production.

Finally, there appears to be some enduring confusion regarding the extent of direct benefits of off-channel habitats to early life stages, specifically in terms of habitat occupancy.  Some years ago, Coutant (2004) published a paper proposing a range of direct benefits of riparian and off-channel habitat features to early life stages of white sturgeon.  This paper suggested that wetted vegetation, newly wetted surfaces, and other physical features of off-channel habitats were needed for survival of early life stages of white sturgeon.  This paper also suggested that the absence of these features was contributing to recruitment failure among populations, since many of the altered large rivers in the Northwest simultaneously exhibited sturgeon recruitment failure and lacked some or all of the important physical habitat and hydraulic features of off-channel habitats.

However, since this paper was published (and even before publication in the form of manuscript review comments) there was and remains an absolute consensus among white sturgeon field researchers throughout the range of the species that planktonic white sturgeon embryos, free embryos, and early stage larvae are constrained hydraulically (and are collected exclusively from) deep water, thalweg habitats.  This contention is supported by the many naturally recruiting populations in altered habitats, which completely lack off-channel habitat (e.g., most lower Snake and Columbia river reservoirs).  Possible exceptions, which we suggest are largely matters of semantics, were previously reported by Perrin et al. (1993) and McAdam et al. (2005), based on studies in the Lower Fraser River in B.C.  These authors reported the use of side channel habitats by early life stages, and suggested the possibility of spawning events in side channel habitats.  However, in these cases, the flow paths between main and side channels were intermingled and braided, providing similar hydraulic and physical habitat conditions in both the main channel and side channels.  In other words, depth, velocity, and substrate conditions associated with main channel habitats appeared similar and available in these “side channels”.  Thus, applying the words “side-channel” of “off-channel habitats” to different rivers may have obfuscated the issue of white sturgeon using similar hydraulic features for successful spawning among rivers in both types of habitat, marginalizing the need for the argumentative distinction.

In summary, habitat restoration actions proposed by this project are designed to benefit all life stages of white sturgeon both directly (by addressing migratory, spawning, and rearing habitat and food availability limitations) and indirectly (by providing habitat diversity and opportunities for off-channel primary and secondary production and food web complexity required to support sturgeon and other fish populations) as well as the other five focal species and other native aquatic populations.  Proposed and implemented project activities are consistent with the needed multi-disciplinary approach to restore sturgeon and the habitats, ecological conditions, food web complexity, biological production, biodiversity, and ecological processes required to support them.

 

The ISRP reviewers note that the sponsors should be complimented for their successful outreach and educational efforts but caution that if the projects start to unravel because of unexpected changes that may affect ecosystem recovery, for example high or low flows, working relationships between parties may be strained and an adaptive management plan that allows for contingency planning is crucial.

This point is exactly why we feel strongly that the feasibility analysis, design and implementation approach we’ve developed, and propose to implement, is robust, efficient and embraces a precautionary approach.  We hope that our explanation of the many activities associated with each step of the feasibility analysis and design process helps the ISRP reviewers to better understand the degree of coordination, review and active involvement with stakeholders that occurs on this project, beyond simply education or outreach activities.  What has been critical to date is to be able to communicate the larger picture to the community, i.e., presenting the community with the Master Plan framework, presenting the community with the Phase 2 concepts, and presenting the community with the phased implementation approach; while also ensuring that each individual project will be implemented in a sequential, deliberate, and adaptive manner with active involvement of landowners, co-managers, agencies and the local community. 

A few additional points in response to the ISRP comment: 

  • We are specifically designing each of the projects for sustainability within a broad range of flows.
  • The KRHRP is designed to address Kootenai sturgeon BiOp attributes in a way that allows for habitat attribute attainment that is biologically meaningful ,while also providing the broader ecosystem-restoration benefits associated with the project.  
  • The community knows about and is supportive of the KRHRP project.  They understand that it will be implemented in a phased manner and that the community and local landowners will be involved at every stage of the process. 
  • Because we aren’t attempting to complete final designs of all the projects at once (which would take a number of years) and then stage permitting and construction after that (which would add more time due to regulatory agency work load limitations and the three month instream construction window), we’re not locked into a specific design that we may want to be able to modify five years later when we get to implementation. 
  • Our design and implementation process is designed to be adaptive at every step of the process.

 

5. Specific comments on protocols and methods described in MonitoringMethods.org

The ISRP reviewers noted that description of the methods on the monitoringmethods.org site were incomplete.

We have added additional detail to complete the descriptions of methods on the monitoring methods.org site.

 

The ISRP reviewers commented that there was no discussion regarding toxic compounds in the river and the potential influence they may be having on the ecosystem.  They suggested that toxic chemicals in the river could be an issue and should be investigated as a part of the monitoring program.  

Contaminant monitoring in the Kootenai River between the Montana border and Kootenay Lake in Canada has been occurring since the 1990s.  Monitoring included collection and analysis of sediment, suspended sediment, water, macroinvertebrates, non-game fish, sturgeon, plankton, and periphyton in order to determine tissue and environmental concentrations of metals from mining and other industrial sources, organochlorine and organophosphate pesticides from agricultural applications, PCBs from industrial sources, pentachlorophenol from breakdown of organochlorine compounds and use in wood preservatives, and polybrominated diphenyl-ethers (PBDEs; fire retardants).  This monitoring program has generally been coordinated with white sturgeon contaminant monitoring throughout the Canadian and US reaches of the mainstem Columbia River. 

Initial research conducted by Kruse (2000) indicated the potential for endocrine and reproductive disruption in Kootenai River white sturgeon due to bioaccumulated PCBs, organochlorine pesticides, and metals.  However, further assessment (Kruse and Fernandez In Progress) revealed that contaminant concentrations are generally lower than those reported for other areas within the middle and lower Columbia River.  Comparison with published literature revealed that while some contaminants detected in tissues and environmental media exceed biological effects thresholds set by United States and Canadian governmental agencies, very few are at concentrations associated with published physiological and environmental effects. 

Chlorine was monitored in surface water from the lower Kootenai River above, at, and below the municipal sewage treatment plant (Kruse 2008a).  Concentrations of total chlorine at the plant outflow exceeded the LC50 for larval Kootenai River white sturgeon (42.3 ug/L; USFWS 2008).  However, chlorine concentrations in samples drawn from upriver and downriver sites were lower than this threshold. 

Metals have been analyzed in water, sediment, suspended sediment, macroinvertebrates, plankton, periphyton, and fish tissues (Bauer 2000, Davidson and Kruse 2006, Kruse and Scarnecchia 2002a&b, Kruse 2003, Kruse 2005, Kruse 2008a&b, KTOI unpublished data, Pocketwater Inc. 1999).  Sediment sampling indicated slight exceedances of threshold effects for DDT, arsenic, cadmium, chromium, lead, mercury, nickel, and zinc.  However, calculation of specific screening tools (Probable Effects Quotients and Theorectical Bioaccumulation Potential) suggested that these sites were “low priority” for remediation and the potential for biological uptake was equivalent to current conditions.  Kruse and Scarnecchia (2002a & b) reported potential relationships between parentally and environmentally derived metals and physiological effects in Kootenai River white sturgeon.  However, recent data collection and analysis revealed only one similar relationship suggesting potential depression of the sex steroid ketotestosterone via zinc.  In general, results from the most recent sturgeon tissue monitoring indicate low concentrations of toxic metals and an unlikely possibility that bioaccumulated metals are affecting reproduction and survival of Kootenai River white sturgeon at this time.  Concentrations of metals in mainstem and tributary waters do not indicate any potential concern with toxicity given the constraints of the field and laboratory methods used (Bauer 2000, Pocketwater Inc. 1999).

Asbestos was analyzed in sediment core samples collected upriver of Bonners Ferry and results revealed two types of asbestos (Chrysotile and Actinolite) in four of 23 samples analyzed (Kruse 2008b).  However, total volume of asbestos was far below the regulatory threshold of 1%.

Organochlorine pesticides and PCB concentrations were analyzed in sediment, suspended sediment, periphyton, plankton, macroinvertebrates, and fish tissue (Davidson and Kruse 2006, Kruse 2003, Kruse 2005, Kruse 2008a&b, Kruse and Fernandez In Progress, KTOI unpublished data).  Results of recent monitoring (Kruse and Fernandez In Progress KTOI unpublished data) suggest that while the organochlorine pesticides DDT (and its metabolites) and endosulfan are contaminants of concern for Kootenai River white sturgeon, these compounds are at fairly low concentrations and no longer being used in the basin; therefore, concentrations will likely continue to decrease over time.  PCB concentrations in tissues exceeded IJC recommended criteria, suggesting potential impacts on piscivorous wildlife.  Concentrations also exceeded effects concentrations reported in published literature (Kruse and Fernandez In Progress).   Due to the fact that PCBs are currently present in equipment used for hydroelectric power generation and other industrial sources throughout the basin, these contaminants remain an issue of concern.

Pentachlorophenol was found at low to undetectable concentrations in Kootenai River white sturgeon tissues (Kruse and Fernandez In Progress).  However, a significant negative relationship was noted between pentachlorophenol and the brain enzyme acetylcholinesterase, suggesting potential nervous system impacts and increased deformity rates in fish.  While deformity rates were slightly higher in juvenile Kootenai River hatchery-reared sturgeon than published average deformity rates for fish, the adult deformity rate was similar to the average rate (Kruse and Fernandez In Progress).

Polybrominated diphenyl-ethers (PBDEs) were analyzed in juvenile sturgeon muscle tissue (Kruse and Fernandez In Progress).  Results revealed concentrations lower than those reported for upper Columbia River white sucker and white sturgeon (Kruse and Webb 2006, Rayne et. al 2003).  The primary source of PBDEs in the Kootenai River appears to be flame retardants and may be negatively impacting female reproduction through inhibition of the yolk protein vitellogenin (Kruse and Fernandez In Progress).  However, published literature was not available to validate this finding.

The potential for effects of organophosphate pesticides on sturgeon physiology was assessed through monitoring for potential inhibition of the brain enzyme acetylcholinesterase (Kruse 2000).  Results did not indicate inhibition of this enzyme, suggesting that organophosphate pesticides are not of concern in lower Kootenai River ecosystem. 

The results of contaminant monitoring in the Kootenai River suggest a relatively healthy and recovering system.  Assessed contaminants appear to be at lower concentrations than those detected in similar media throughout the mainstem Columbia River system.  Although lack of published research pertaining to some of the compounds and synergistic effects of multiple compounds limits definitive assessment of effects, current data suggest that contaminants are not a significant limiting factor for the Kootenai River ecosystem. 

 

Regarding critical uncertainties research the ISRP reviewers asked if ELS research will be included as part of the RME effort and expressed concerns about the reliability of fin ray geochemistry.

We agree with the ISRP about the importance of RME to provide information about critical uncertainties and that is why we have proposed the ELS research for white sturgeon and the side channel research.  These areas have been identified as information gaps that are not being filled by the RME in other projects.  The monitoring and evaluation of sturgeon spawning and recruitment is implemented by Idaho Fish and Game – Project 198806500 and results are used by the Tribe and other agencies to assess fish response to flow management and habitat conditions in the Kootenai River.  Additionally, the Tribe, IDFG, and BCMFNLRO are collaborating on the development of an RME plan for burbot in the Kootenai.  Various other programs and projects are also monitoring fish in the Kootenai.  We do not want to duplicate effort, but rather, build upon the RME already taking place by filling in the gaps.  And as we coordinate through our Adaptive Management process that we described in the previous section, we will be able to continue to refine the RME for this project.  Additionally, we agree with the ISRP that the information from the ELS and side channel research needs to be incorporated into the RME program and we plan to do that, in cooperation with IDFG.  As for the fin ray geochemistry component of the proposal, the project sponsors recently found out that funding for fin ray research has been provided by a different funding entity.  We had initially included it as part of this proposal because it had been identified as a high priority by the USFWS White Sturgeon Recovery Team, but we understand the ISRP’s concerns about the reliability of this technique and we do not plan to incorporate it into our project at this time.

Closing comments

In closing, we would like to thank the ISRP for the opportunity to provide additional information and clarification for your consideration during your final review of this important project.  We hope you find that we have addressed your questions adequately.  Thank you.

 

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[1] Al-Chokhachy et al. (2010) stated that they found only one article (Jakober et al. 1998) that dealt with bull trout habitat associations in lower-most reaches (i.e., larger river reaches); however, Jakober et al. (1998) addresses headwater tributaries, not lower river reaches.  Conversely, in the Al-Chokhachy et al. (2010) reference, they cite two articles dealing with bull trout rearing in large mainstem river systems, which are Muhlfeld et al. (2003) and Muhlfeld and Marotz (2005) concerning subadult bull trout seasonal movement and winter habitat use in the mainstem Flathead River (MT).