NOTE TO CONTRACT OFFICER:  Please send contract documents to Jannice Richardson, Administrative Contact and Matt Boyer, Contract Manager.

PROJECT BACKGROUND

Fisheries losses caused by the construction and operation of Libby Dam, site-specific mitigation actions and monitoring strategies were documented in the Libby Dam Fisheries Mitigation and Implementation Plan (MFWP et al. 1998).  As directed by the Northwest Power and Conservation Council's (NPCC) Fish and Wildlife Program (NPCC 1994 and 2000), the Mitigation Plan and Kootenai Subbasin Plan document present actions needed to offset fisheries losses associated with the construction and operation of Libby Dam. These documents were developed collaboratively with the Confederated Salish and Kootenai Tribes (CSKT), the Kootenai Tribe of Idaho (KTOI), and Montana Fish Wildlife and Parks.  Mitigation actions are also coordinated with the Idaho Department of Fish and Game (IDFG) and British Columbia Ministries.

This program implements the NPCC Plan to enhance hydropower-affected fish stocks in the Montana portion of the Kootenai Watershed.  Fish restoration efforts in this work plan are consistent with the White Sturgeon Recovery Plan (USFWS 2019) and the White Sturgeon Biological Opinion (BiOp) on the operation of the Federal Columbia River Power System (FCRPS).  Kootenai River white sturgeon (Accipenser transmontanus) are endangered, with approximately 1,000 wild individuals remaining (Beamesderfer et al. 2009). Bull trout (Salvelinus confluentus) are listed as threatened under ESA, and populations in the Kootenai River were fragmented by Libby Dam.  This project implements bull trout restoration efforts that are consistent with the Bull Trout Recovery Plan (USFWS 2015), including restoration and protection of stream segments within streams identified as critical habitat (USFWS 2010) to ensure connectivity to and enhancement of core bull trout spawning and natal tributaries within the Kootenai Subbasin.  The abundance and distribution of westslope cutthroat trout (Oncorhyncus clarki lewisi) and redband trout (O. mykiss) in the Kootenai Basin have declined from their historic condition due to dam construction and operation, negative interactions with nonnative species (e.g. predation, competition, genetic introgression), and anthropogenic factors (e.g. channel alterations and sedimentation). Hybridization and competition with non-native fish species and habitat degradation pose the greatest threat to westslope cutthroat and redband trout.   This work plan implements and evaluates on-the-ground habitat enhancement efforts that alleviate limiting factors to native species populations.

Project History  

This project combines the former projects 1983-465-00, 83-467-00, 1994-010-00, and 2006-008-00 for efficiency and cost savings.  Work on Libby Reservoir to assess the effects of operation on fish populations and lower trophic levels began in 1982.  This project established relationship between reservoir operation and biological productivity and incorporated the results in the computer model LRMOD.  The models and preliminary IRCs (Integrated Rule Curves, originally called Biological Rule Curves) were first published in 1989 (Fraley et al. 1989), and then refined in 1996 (Marotz et al. 1996 and 1999).  The IRCs were adopted by NPPC in 1994 but were superseded by operations called for by the NMFS 1995 Biological Opinion.  Although the IRCs were not ever fully implemented, many of the concepts were adopted in the NPCC’s 2004 operating strategy known as the Mainstem Amendments, which were first fully implemented in October 2008.  This project works closely with many efforts within the Kootenai Basin for cost savings efficiency.

The Libby Mitigation Project established a long-term database to monitor population trends for kokanee, bull trout, westslope cutthroat trout, rainbow trout, burbot and other native fish species.  Long-term monitoring programs of zooplankton and trophic relationships were similarly established.  A model was calibrated to estimate the entrainment of fish and zooplankton through Libby Dam as related to hydro-operations and use of the selective withdrawal structure. Research on the entrainment of fish through the Libby Dam penstocks began in 1990, and results were published in 1996 (Skaar et al. 1996). The effects of dam operation on benthic macroinvertebrates in the Kootenai River was also assessed (Hauer et al. 1997) for comparison with conditions measured in the past (Perry and Huston 1983).  This study was replicated in 2005 with the addition of examining the effect of a nuisance diatom Didymosphenia geminata (D. geminata) on the benthic community (Marshall 2007).  The Libby Project has also identified important spawning and rearing tributaries and conducted genetic inventories in the Montana portion of the Kootenai Watershed for bull, westslope cutthroat, and redband trout.  This project developed a non-lethal genetic methodology to differentiate between native redband trout and non-native rainbow trout (Brunelli et al. 2008), and a non-lethal genetic methodology to identify natal tributary origin for bull trout in the upper Kootenai Watershed and quantify bull trout entrainment at Libby Dam (Ardren et al. 2007; DeHaan et al. 2008; DeHaan and Adams 2011).   Research on the effects of operations on the river fishery using IFIM techniques was initiated in 1992. The results of this study were recently finalized and upgraded with the incorporation of GIS technology (Miller and Geise 2004). The final result was a model capable of graphically and numerically quantifying weighted usable area for juvenile and adult rainbow trout and bull trout in the Kootenai River for a wide range of discharges.  

Scientific Framework

We have designed our program to address fisheries issues in varying levels of scope, descending from basin-wide, over-arching mitigation requirements to site-specific actions.  Mitigation projects are selected and prioritized primarily on the Kootenai Subbasin Plan.  We have further outlined our rationale and decision pathway within this document (see below).  The scientific framework addresses varying levels of scope, progressing from basin-wide issues toward site-specific details. Each level is addressed by individual mitigation actions. Our priority is to prevent impacts that can reduce the overall health of the subbasin.  Basin-wide issues include federal and private dam operations and the prevention or containment of invasive aquatic nuisance species. Onsite mitigation addresses habitat degradation, fish passage barriers, genetic introgression with pure native fish stocks and negative interactions between native and nonnative fish species. Offsite mitigation presents opportunities to create genetic reserves to conserve native species and to increase angling opportunities.

Modifications to dam operation are a basin-wide mitigation requirement because of the far-reaching influence of dam operation on environmental conditions in the reservoirs and rivers throughout the Columbia River Basin. Montana has actively pursued a basin-wide operating strategy beneficial to imperiled fish stocks in the Columbia River headwaters, as well as the lower Columbia River. In the Libby Mitigation Plan, we estimated that approximately half of the losses identified within the loss statement (MFWP et al. 1998) could be mitigated by modifying dam operation.  Much of the remaining losses can be mitigated using techniques that do not require changes in reservoir or river management.  The overall goal of the Libby Mitigation Project is to correct effects caused by the Federal hydropower operations and mitigate for fisheries losses attributed to the construction and operation of Libby Dam using watershed-based, habitat enhancement, fish passage improvements, and offsite fisheries habitat improvement measures. The Libby Mitigation Project's Work Elements for the current funding cycle have been organized around the following objectives.  

Objective 1:  Evaluate impacts of Libby Dam operations on resident fish populations and the food web that supports these fish and their habitats and develop implementation strategies to alleviate limiting factors.

Mitigation measures that reduce the impacts of the continued operation of Libby Dam are most effective when reservoir and river management can be modified to offset onsite impacts.  Montana has embraced this strategy and played an important role in developing operational recommendations at Libby Dam.  This overall strategy was also the basis of the development of the Libby Mitigation Plan (MFWP et al. 1998) and the Kootenai Subbasin Plan (KTOI and MFWP 2004).  However, operations at Libby Dam have changed substantially since these documents were developed (Sylvester et al. 2016).  

Libby Dam and the reservoir behind it traps and retains 80-93% of the total phosphorus and 13-34% of the total dissolved inorganic nitrogen (Yassien and Ward 2018). Winter D. geminata and summer phosphorus have been demonstrated to be the most parsimonious covariates negatively related to annual growth of rainbow trout in the Kootenai River downstream of Libby Dam (Dunnigan and Terrazas 2021).  MFWP used these results as the basis for a proposal to implement an experimental nutrient addition project (MFWP 2022a and 2022b).  The U.S. Fish and Wildlife Service’s (Service) recent Biological Opinion (BiOp) on Columbia River System (CRS) – Operations and Maintenance of 14 Federal Dams and Reservoirs includes a term and condition (T&C) for the Action Agencies (BPA, Bureau of Reclamation, and the Corps) to work with MFWP to implement a nutrient addition project in the Kootenai River near Libby Dam. Specifically, T&C 17.2(2)(e) states, “Within two years of the issuance date of this Opinion (i.e. July 2022), the Action Agencies shall work with the Service and MFWP to assess the benefit of adding nutrients to the Kootenai River near Libby Dam to improve primary productivity for bull trout forage and to develop and implement a plan for improving nutrient conditions in the Kootenai River through December 2025. This experimental nutrient addition project will require additional baseline data collection during this contract period, including benthic invertebrate (WE K), water quality, benthic periphyton and D. geminata (We J), and resident population metrics (WE L).  The nutrient addition experimental project will require a facility to house the infrastructure required to deliver the nutrient product to the Kootenai River.  This work will be a collaborative effort between the Federal Action Agencies and is identified in WE Q. Research into factors correlated with primary and secondary productivity in Libby Reservoir are an ongoing applied research effort and are identified in WEs H and I.  

Objective 2:  Restore, enhance, or protect and maintain existing sustainable native fish populations and their habitat in the Kootenai Basin to mitigate for losses attributable to the construction and operation of Libby Dam.

The Libby Mitigation Project has a solid track record of achieving effective mitigation projects within the Montana portion of the Kootenai Subbasin (see project history in Dunnigan et al. 2021).  We continue to improve existing habitat conditions within the basin through our proactive restoration program.  Our program plans to continue our ongoing long-term multi-year revegetation efforts on the previously completed Therriault Creek restoration project during the next year (WE O).
The Ten Lakes Scenic Area is in northwest Montana, and lies within the Wigwam River watershed. This mountainous region contains several lakes of which the historic fish distribution was previously unknown. However, over the past several years this project has collected inventory data to determine that most of these lakes contain only minor remnants of non-native fish stocked during the past century.  However, Rainbow Lake is an exception to this, containing a self-sustaining population of predominantly Yellowstone Cutthroat Trout.  Surface water connection to downstream waters has prompted us to prioritize the removal of these fish to prevent downstream hybridization with westslope cutthroat trout.  The removal project is expected to occur in fall of 2023 (WE E) with the planning and environmental compliance for this work is identified within WEs B and E.  

A similar scenario exists in several mountain lakes within the Cabinet Mountain Wilderness area.  The historic fish distribution of the Cabinet Mountain Lakes is unknown but we speculate that these lakes were either fishless or contained westslope cutthroat trout or redband trout.  Our project completed work during the previous two contract periods to partially evaluate the status and distribution of native fish species occurring within the watersheds, but additional assessment work is needed to further investigate existing native fish distributions for restoration opportunities and donor stock identification.  This work is identified in WE N.    

Objective 3:  Collect, analyze and interpret spatial distribution, seasonal movement, population trend, and growth data, absolute and relative abundance indices, and genetic and life history information needed for the conservation and recovery of native resident fish species, as outlined in the Libby Mitigation and Implementation Plan (MFWP et al. 1998) and Kootenai Subbasin Plan.

Understanding the limiting factors of native species requires fundamental information related to the trend and status of those species.  Therefore, we propose the following assessments to understand trend and status of bull trout, burbot and Kootenai River white sturgeon.  Montana FWP has developed several monitoring strategies specifically designed to investigate the life history and limiting factors of bull trout within the Kootenai Subbasin.  We have documented that hydro operations at Libby Dam are responsible for substantial bull trout entrainment (Ardren et al. 2007; DeHaan and Adams 2011).  Several work elements are intended to further monitor the levels of impact of hydro operations on the bull trout populations in the Kootenai River below Libby Dam.  Work Elements are also included within this SOW that are intended to quantify bull trout relative abundance through redd counts and habitat related factors (WE G).  

The production of phytoplankton and invertebrates represent the lowest levels of the food web that provides forage for many of the species of fish in Libby Reservoir. Available nutrients (total nitrogen and phosphorus) and water residence and retention time in reservoirs has been shown to be important factors that influence productivity in reservoirs (Kimmel and Groeger 1984). Yet, substantial changes in both of these determinant factors have occurred since the last productivity estimates on Libby Reservoir (Ward and Associates 2015; and Sylvester et al. 2018). Work identified in WE H will estimate current primary (Chl a) and secondary (zooplankton) productivity in Libby Reservoir and compare those estimates to the previous work which will provide valuable insight into the productive capacity of higher trophic levels within the reservoir. Estimates of primary and secondary productivity in Libby Reservoir are necessary to understand trend and status of several focal species inhabiting the reservoir (WE I).
Montana FWP estimates burbot relative abundance directly downstream of Libby Dam annually using baited hoop traps.  This work will continue and is identified in WE L.  Similar work occurs within Libby Reservoir every two years and is identified in WE I. The Kootenai River in British Columbia, Idaho, and Montana contains a unique landlocked population of white sturgeon that has been isolated from anadromous Columbia River and other white sturgeon populations since the last ice age (Northcote 1973). The Kootenai River population is currently restricted to 270 km of river between Kootenay Lake, B.C. and Kootenai Falls.  This population differs from other populations of white sturgeon by being landlocked, less genetically diverse, and tolerant of colder water temperatures, and is currently listed as endangered under the Endangered Species Act due to consistent low levels of juvenile recruitment since the 1960’s (USFWS 2019). Until recently, little information existed regarding white sturgeon in Montana when Montana FWP began population assessment work in the Montana portion of the Kootenai River.  The goals of this work are to 1) assess the status of white sturgeon in the Montana portion of the Kootenai River and 2) supplement ongoing monitoring and recovery efforts in Idaho and British Columbia. The four primary objectives of the study are:
1. Assess the current structure (age, length, wild vs. hatchery) of the white sturgeon population in the Kootenai River, Montana and describe their abundance
2. Describe growth and condition indices for white sturgeon in Montana
3. Identify movement patterns and evaluate long-term residency of white sturgeon in Montana
4. Assess the potential for natural reproduction and recruitment of white sturgeon in Montana
This work continues and is identified in WE M.  

Objective 4:  Evaluate the efficacy of the Kootenai River Ecosystem Project currently being conducted at the Montana/Idaho border by the Kootenai Tribe of Idaho and Idaho Fish and Game.  

The Kootenai River Ecosystem Project is a collaborative venture between the Kootenai Tribe of Idaho (Project 199404900) and Idaho Fish and Game (Project 198806500) intended to restore the productivity of the Idaho portion of the Kootenai River due to the loss of nutrients trapped by Libby Dam.  Montana FWP contributes to this cooperative project by conducting fish sampling at a control site located upstream of the nutrient addition site (Hardy et al. 2020).  These work activities are identified in WE L Milestone H.  

Objective 5:  Summarize, evaluate, analyze, discuss and disseminate information gathered during project activities in a scientific format.  

This work will be accomplished primarily through public meetings, project annual reports, and status reports, and is identified under WEs P and R and various milestones under most WEs that include making datasets publicly accessible.