The ISRP found this a difficult project to review without a site visit, given the collaborations with multiple partners. Nevertheless, the ISRP recommends that this project Meets Scientific Review Criteria with three conditions, all of which should be addressed in the next annual report and work plan:

1. SMART objectives. Establish SMART objectives for the Ecosystem Monitoring Program (EMP) objectives, as much as possible, including succinct empirical statements of expected outcomes (with timelines).
2. Benefits to fish and wildlife. Develop a strategy for collecting, analyzing, and reporting information to quantitatively demonstrate benefits to fish and wildlife from restoration and protection actions.
3. Budget. Remove the proposed carbon sequestration study (Objective 7) from the budget and the budget justification.

The ISRP also has a recommendation for the proponents, but it is not a condition. The monitoring data do not appear to be used to in a model that could predict responses or conditions at other estuarine sites within this geographic area. If this is correct, then we encourage the proponents to develop a strategy for constructing such a model, which could be an important tool for understanding the effectiveness of estuarine restoration efforts.

In our preliminary review, we requested responses on the following nine topics. Our final comments follow each item:

1. SMART Objectives. While the proponents made the goals and objectives for the two monitoring programs somewhat clearer, they did not establish SMART objectives for the EMP, which remains unnecessarily vague. Even though the EMP requires multiple partners to complete the monitoring protocol, this should not preclude establishing SMART objectives for their collective actions and requiring partners to develop SMART objectives for subprojects. The ISRP expects the lead project to be responsible for seeing that all partners submit analyses in a timely manner. The ISRP has requested other large, coordination projects to provide similar SMART objectives and assist partners in developing SMART objectives (e.g., Grande Ronde Model Watershed, Upper Columbia Programmatic Habitat).
   
   An attempt should be made to put the objectives into a SMART format as much as possible. For instance, EMP Objective 1 could be revised as follows: “Monitor status and trends in ZZ characteristics of the of biogeochemistry of mainstem surface waters of the lower Columbia River estuary at XX sites at YY times annually, as well as at XX sites and YY times above the confluence with the Willamette River. These data will be used to quantify the impacts of tidal seawater fluxes and environmental change on habitat capacity for juvenile salmonids.”
   

   No attempt is made to provide succinct empirical statements of expected outcomes (with timelines). One would expect the proponents to provide reasonable projections of expected changes, especially since the project has been active for more than 20 years.

2. M&E Matrix – Lead. In the revised proposal, the proponents provide tables of locations, sampling levels, and metrics for each level of Action Effectiveness Monitoring (AEM), as well as the partners responsible for specific M&E efforts. The project has previously submitted these tables and figures in annual reports to BPA for its regular update of the Columbia Estuary Ecosystem Restoration Program (CEERP) Plan. Notably, the proponents also give this information in a timely manner to their partner projects, including CREST, CLT, WDFW, and CIT. The proposal describes the monitoring methods, analyses, and specific metrics for each overall monitoring objective and provides supporting documentation and links to MonitoringResources.org. The proponents work with their partners to produce a State of the Estuary report to USEPA every five years. The most recent report (2020) includes a story map with spatially explicit information on land use, ecological conditions, project accomplishments, and monitoring results for water quality and habitat conditions. The 2020 State of the Estuary Report is comprehensive yet concise, and the story map is an exceptional contribution to better understanding the complex nature of the estuary and the monitoring and restoration program. 
   
   
3. Project Evaluation and Adjustment. The proponents’ response generally addresses the ISRP concerns. However, it remains unclear when an AEM protocol can be discontinued. Table 4 (p. 37) lists the schedule for when AEM activities are to occur but not when they can be discontinued. Perhaps it is not possible to determine when an activity can be terminated (for both AEM and EMP) since no quantitative levels are established to judge if the restoration actions or the environmental conditions are deemed adequate or successful. The proponents should consider how “success” is determined so that specific monitoring activities can be discontinued or transferred to other sites. The program also should consider establishing “thresholds of probable concern” for some environmental characteristics. If measurements consistently fall below a pre-established, ecologically acceptable level (threshold), then resources could be transferred elsewhere for monitoring other important parameters.
   
   
4. Carbon Sequestration and Methane Fluxes. The proponents removed this activity from the proposal. However, the proposed carbon sequestration study (original Objective 7) still needs to be removed from the budget and the budget justification. 
   
   
5. Discussion of Toxic Chemicals. The ISRP is pleased to see that the Problem Statement section has been revised significantly, including the discussion of toxic chemicals, and that readers are now referred to the habitat restoration proposal (200301100) for more information on limiting factors and threats within the lower Columbia River region. 
   
   
6. Accounting for Changes in (Land Use) Development. The proponents’ response revealed a major information gap for the lower Columbia River. Recent changes in land use in the geographic area have been substantial, especially in close proximity to the river and tributaries. These land-use changes have significant environmental impacts on the Columbia Estuary and associated habitats, even with existing riparian protections. That said, the ISRP is impressed by the information and analyses presented on land use in the 2020 State of the Estuary report using the limited available data. We encourage the proponents, and the states of Oregon and Washington, to seek support for expanding the land-use analyses, which are essential for developing a better understanding of causes for change in the estuary as well as for predicting environmental future changes. The ISRP encourages the Council staff to convey the importance of this informational gap to BPA and other regional agencies with restoration activities in the estuary.
7. Evaluation of Disturbed Sites. The proponents provide a reasonable response to the ISRP query about expanding the monitoring program to sites significantly altered by human actions. Because funding for EMP and AEM is capped, we agree that the best strategy is to remain focused on minimally human-altered habitats as they provide a suite of reference sites for restoration designs and actions.
   
   
8. Benefits to Fish and Habitat. The response by the proponents is concerning to the ISRP. Despite substantial long-term funding for restoration and protection of juvenile salmonid habitat, the project does not, nor do the other estuary projects (CREST, CLT, WDFW, CIT, LCEP restoration projects), quantify the benefits to fish from the habitat restoration (e.g., total abundance, size at smoltification, or survivorship). The ISRP agrees with the proponents that this is an important, and essential, information gap to fill in order to evaluate the usefulness of many of the restoration and protection actions. A starting point could be to use the recently completed 2020 PNNL and NMFS diagnostic study to document that restoration provides immediate benefits to juvenile salmon and steelhead using the lower Columbia River. The ISRP encourages the proponents to partner with the appropriate agencies and groups in the very near future to see that appropriate monitoring data are collected to demonstrate that habitat restoration and protection are benefiting juvenile salmonids. In order words, the proponents should develop and implement a strategy for collecting the necessary information.
   
   A related concern is that the monitoring data do not appear to be used to populate a model that could predict responses or conditions at other estuarine sites within this geographic area. The proponents note that the data are used to assess habitat capacity within a site (p. 23), but it is unclear how the data are used to accomplish this. Further, the proponents note (p. 24) that data collected under Objective EMP 4 are analyzed in conjunction with data collected under the other objectives to determine relationships between habitat structure, capacity, and juvenile salmonid habitat usage – and the findings are used to assess juvenile salmon habitat usage throughout the lower Columbia River and in comparisons with restoration sites. The ISRP would expect that this would be well known after 18 years of research and monitoring. Yet, there is no mention in the proposal that the data are used to populate a predictive model, one that is powerful enough to be used more widely in the estuary. Is there a model that uses the information to predict the fish capacity of the site, or environmental conditions? If not, then one is needed if only to synthesize the two decades of information already acquired.
   
   Note: The Jeffres et al. (2008) study is impressive but took place under experimental conditions in rice fields of a highly altered California river. The ISRP wonders to what extent this study is applicable to the lower Columbia River.
   
   
9. Process for Determining Number of Monitoring Sites. The proponents’ response to this concern is adequate. Since monitoring funding is capped, a Steering Committee composed of BPA, the USACE, and LCEP guide the prioritization of AEM levels to individual restoration sites. This appears to be a reasonable approach.

Specific Comments:

1. EMP Goal 3 (p. 20) cannot be accomplished without a quantitative analyses of spatial trends in land use associated with the river/estuary. The Goal needs to be re-worded to reflect what is actually being investigated.
2. The use of the term “biogeochemistry” throughout the proposal is vague, and therefore confusing as to what is actually being monitored. It needs to be clearly defined early in the proposal or another, more appropriate, term or terms used.
3. The ISRP agrees that vegetation composition is important for the production of organic matter (released to the river in the form of macrodetritus, p. 32). However, the proponents should consider monitoring microdetritus (< 1 mm diameter) and dissolved organic matter (< 0.5 um). These are the dominant sizes, in terms of mass, of detritus exported to the river. Further, DOM reacts quickly with seawater at low salinities to become biologically available to the foodweb.
4. The abundance of pelagic zooplankton (p. 33) is not a valid method for estimating secondary production. The description of the method should be revised to reflect what is actually measured, zooplankton abundance. If the project needs estimates of secondary production, another method should be used.

Preliminary ISRP report comments: response requested

Response request comment:

The project has been highly productive for many years, providing monitoring for restoration activities conducted throughout the Lower Columbia River. The proponents have received high marks from the ISRP during past reviews for their comprehensive approach. Despite the proponent’s strong track record of accomplishments, the proposal’s length and inclusion of too much previous work make it difficult for reviewers to differentiate past results from actions being proposed for the next funding cycle, and to evaluate if the activity needs to be continued or if enough has been learned so that the activity can be deemed successful, and thereby considered complete. It would have helped greatly if the proponents had adhered to the suggested guidelines for proposal preparation. In addition, the proposal did not adequately tie together the monitoring actions with the roles of other estuarine restoration groups. For instance, often it was not clear how specific monitoring activities informed other projects.

The Columbia River estuary is ecologically important and is highly altered by multiple processes, including dams and processes unrelated to dams. Therefore, assessment and monitoring of the numerous restoration actions are surely warranted. The proposal gives the appearance of seeking to measure everything, without specific motivating hypotheses and questions. Some baseline monitoring is understandable, but given the many levels of complexity and variation in the estuary, greater focus would be beneficial. The proposal's two major programs—Ecosystem Monitoring (EM) and Action Effectiveness Monitoring (AEM)—could be better integrated, and the Ecosystem Monitoring could use clearer goals.

The ISRP requests the proponents to address the following points in a revised proposal and to provide a brief point-by-point response to explain how and where each issue is addressed in the revised proposal:

1. SMART objectives. Provide succinct objectives in a SMART format (see proposal instructions), as well as succinct empirical statements of expected outcomes (with timelines). 
   
   
2. M&E matrix - lead. One of the challenges for ISRP reviewers is understanding the specific monitoring that is being conducted for multiple implementation projects. Habitat restoration projects or hatchery projects implement actions that are intended to address limiting factors and benefit fish and wildlife. Most of these projects do not directly monitor habitat conditions or biological outcomes, but most identify other projects in the basin that monitor aspects of physical habitat or focal fish species. The monitoring project(s) in the basin provides essential monitoring data for habitat, juvenile salmonid abundance and distribution, outmigration, survival, and adult returns for salmon and steelhead. Some monitoring projects focus on status and trends in basins, while others focus on habitat relationships and responses to local actions. It is unclear what monitoring the project(s) conducts for each implementation project.
   
   Given the regional leadership responsibilities of this programmatic project, the ISRP requests the Columbia River Estuary Ecosystem Monitoring Project (200300700) to summarize the linkages between implementation projects and monitoring projects in the Lower Columbia geographic area. The summary should provide a table or matrix to identify what is being monitored for each implementation project and where and when the monitoring occurs. The summary also should explain how the projects are working together to evaluate progress toward addressing limiting factors and identify future actions. A map or maps could help identify the locations of monitoring actions. The monitoring information should clearly explain whether the biological monitoring is local information for the specific implementation site or basin scale monitoring of status and trends or fish in/fish out. We are asking implementation and other monitoring projects to assist your project in producing this summary. 
   
   
3. Project evaluation and adjustment. Provide a brief narrative of how information generated from this project informs an adaptive management process, both for improving monitoring activities and for modifying specific restoration activities. Explain how the project determines when monitoring has been completed for a specific objective and can be discontinued. 
   
   
4. Carbon sequestration and methane fluxes. While the importance of understanding carbon sequestration is clear, folding Objective 7 into this project seems to represent a major shift in focus. Objective 7 requires different types of monitoring than what is already occurring, and it is not clear whether or not it requires different expertise than what the project currently contains. Would the addition of this objective diminish the ability of the program to address the first six objectives? Unless a clear link can be established showing tangible benefits to fish and wildlife, the proposed new activity, measuring carbon sequestration and methane fluxes, should be removed from this proposal and funding sought from another source. 
   
   
5. Discussion of toxic chemicals. The ISRP agrees that the presence and accumulation of toxic chemicals in the estuary are vitally important to ecosystem and salmonid recovery. However, this topic is not specifically addressed by the monitoring or research program since BPA currently does not fund monitoring for toxins in the estuary. As a result, the ISRP considers a discussion of toxins in the Problem Statement to be tangential. The discussion of toxins should be moved from the Problem Statement to the section on Confounding Factors. 
   
   
6. Accounting for changes in development. The overview states, “Presently, we are not tracking whether our restoration activities are keeping up with urban, industrial, or residential development or the conversion of native habitats to impervious surfaces.” If changes in development are not being accounted for, then it is not clear to the ISRP how the effectiveness of restoration actions can be monitored. This should be clarified since it calls into question the ability to evaluate restoration efforts.
7. Evaluation of disturbed sites. The overview states that the focus of the project is on minimally disturbed, tidally influenced emergent wetland sites. While this is important, it is not clear if disturbed sites are also being evaluated for comparison. In the confounding factors section, the proponents note that it may be necessary to broaden sampling efforts to assess “working lands and other less than optimal habitats.” Understanding how monitoring results for minimally disturbed locations compares with disturbed locations seems key to a program intended to evaluate restoration actions. Given this basic need, the proposal should describe how the additional sampling could occur. 
   
   
8. Benefits to fish and habitat. In the section entitled Progress to Date, some broad benefits to salmon and steelhead are described, but it is not always clear if these are tied to quantitative measures of the fish or to habitat actions taken at specific locations. More information on this is warranted. 
   
   
9. Process for determining number of monitoring sites. How are numbers of sites determined each year (see Table 5)? Fewer sites will be sampled in 2022 than in previous years, for example. Factors that determine differences in sample sites each year should be explained. Processes for evaluating and adjusting the project are not fully described and seem to occur informally. It would be helpful to describe the specific meetings in which the focus is in on evaluation versus outreach.

Q1: Clearly defined objectives and outcomes

The Problem Statement had a suggested length of 2 pages or less, but this ran from pages 4-18 including figures. It would be helpful if proponents could more closely adhere to the formatting suggestions and better focus their narrative. As it stands, this section includes many details on methods that would better be presented elsewhere. This excessive length makes it difficult to discern the essential objectives, as well as the fundamental questions and hypotheses driving the work. The importance of estuaries for salmon is well known, as is the degradation of the Columbia River's estuary and the importance of long-term monitoring. Similarly, the statement of Goals and Objectives is too long and includes many details on methods that obscure the goals. The project is so large and complicated that efforts should be made to streamline the proposal and focus on essential information and applications.

The objectives and outcomes are buried in the details. For instance, the information needed, for the most part, to articulate SMART objectives is relegated to the narratives. It should be provided as succinct SMART statements that can be used for future evaluation.

While the authors describe value in integrating climate adaptation and mitigation measures into the project, it would be helpful to understand what (if any) aspects of the current monitoring efforts would be lost if this work was added. Would this change the focus of ongoing efforts by the EMP or the AEM?

An excessive amount of information is included in the problem statement. Presenting a more succinct summary of the need for the program would be helpful as would potentially including information in tables or figures.

In the section on Progress to Date, some broad benefits to salmon and steelhead are described, but it is not always clear if these are tied to quantitative measures of the fish or to actions taken at specific locations. More specific information in the Progress to Date section is warranted.

Q2: Methods

The methods are based largely on established best management practices and are reasonable for the actions being proposed.

While the methods are sound, the questions motivating them are not always clear, contributing to a sense of a program that is very large and growing, with an increasingly broad scope. Many details are presented related to a large number of objectives (biogeochemistry, nutrient cycling, fish sampling, contaminants, temperature, flow).

In terms of details, is there a reason why stable isotope (SI) data are collected at lower trophic levels but not included among the metrics for the fish, or in Table 3? One would think collecting diet, lipid, and SI data from the fish would be standard. Perhaps this is done but not mentioned?

Building on a point in the previous section, the emphasis on sampling undisturbed sites seems to limit the ability to understand if restoration actions are effective.

Q3: Provisions for M&E

The proponents have a strong record of analyses, presenting results at numerous meetings and conferences, as well as conferring with colleagues on related estuarine projects. Nevertheless, it is not clear how the lessons learned are inserted into a formal Adaptive Management process. It also is unclear how the proponents determine that enough has been learned from a specific monitoring activity so that the activity can be considered complete. Are hypotheses being tested or quantitative objectives that are achieved? A discussion focused on determining when the monitoring has completed a specific objective – and thus can be discontinued – would be helpful.

Given the level of detail in other sections of this proposal, the section on Project Evaluation and Adjustment Process is overly brief. It consists primarily of a list of work groups and conferences but does not indicate feedback loops between data being collected and actions, implementations, adjustments to sampling plan, and so forth. Formal processes for evaluating and adjusting the project should be fully described.

Q4: Results – benefits to fish and wildlife

The importance of estuaries to salmonids, the alterations to the Columbia River estuary, and the needs for assessment and restoration are obvious, though certainly not all species and life history types benefit equally. However, the proposal does not make sufficiently clear how the monitoring results will be used and how benefits to fish and wildlife will be assessed. Perhaps this is regarded as self-evident, but the already broad program is proposed to grow even broader to include methane emissions and carbon sequestration, so it is incumbent on the proponents to justify in more detail how the status quo, as well as the expansion, will benefit fish and wildlife.

The proponents have demonstrated in past reports and analyses the potential benefits for fish and wildlife from the restoration activities. While benefits to fish and wildlife are likely, the authors should attempt to support the program’s benefits with more quantitative measures of changes occurring over time as a result of the collective restoration actions.

There is a new activity – measuring carbon sequestration and methane fluxes – proposed along with a request for additional financial support. The ISRP feels this is an important research activity that will produce useful scientific information that will be broadly used in climate mitigation. However, it is not apparent how this information will be used to protect or enhance estuarine fish and wildlife. The ISRP feels that the proponents should seek funding elsewhere for these new activities.

The proposal’s introduction discusses toxic chemicals, a monitoring component that could generate information helpful to assessing the benefits restoration actions for estuarine salmonids. While vitally important to ecosystem and salmonid recovery, this topic is never addressed by the monitoring or by the research program. The ISRP understands that BPA declines to fund such an activity. The ISRP feels that it should be part of the monitoring program and encourages the proponents to add it as a specific objective in the proposal (and for BPA to provide interagency support and funding), even if funded from another source.

 

This is a worthwhile project that promises to provide vital information necessary to recovery of estuarine habitats and improvement of estuarine survival of salmonids. However, the ISRP recommended one major qualification and concluded one particular task did not meet scientific review criteria, as follows:

Qualification: The proponents should prepare a synthesis and integration of results (as mentioned in Objective 2, Deliverable 6), detailing major conclusions after the estuarine classification system is completed and a monitoring design is fully developed, preferably at the end of 2011. Preparation of this document should involve all the partners (NOAA, PNNL, Columbia Lands Trust, Columbia River Estuary Study Taskforce) and should also include methods and monitoring protocols from all subcontractors. The synthesis should be reviewed by the ISRP.

In Part: Objective 1, Task 1 (g) - Does not meet review criteria

“Evaluate the historic shift in base of salmon food web from macrodetrital to microdetrital sources and terrestrial versus marine derived organic matter sources.” A version of the proposal for this subproject was requested in the 2007/2009 project solicitation (200702600-Historic Changes in Organic Nutrient Sources and Productivity Proxies in the Columbia River Estuary in Relation to Juvenile Salmon Habitat Restoration Priorities). The ISRP concluded the project did not meet review criteria primarily because of weak application of the data to management actions, and this comment is still valid.

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

The proposal is very significant to regional programs and describes a key project for implementation of the BiOp. The project is responsive to many regional programs/plans - 2008 BiOp (many RPAs), NOAA’s recovery plan for the estuary (Estuary Module, in press), MERR, and the NPCC Research Plan (regarding the overall estuary program). However, connections to estuary-wide goals of other agencies, such as the 16,000 acre restoration goal of EPA described at the September 2009 Astoria Science-Policy meeting, are not evident.

2. History: Accomplishments, Results, and Adaptive Management

The project has a list of impressive accomplishments that should contribute significantly to improving understanding of estuarine ecology and serve as a basis for estuarine restoration efforts that should benefit salmon. Specific results were sometimes lacking, but this can be expected for a project of this scope. The proponents’ publication record can be improved; more documentation in the proposal is needed on results as the ISRP should not have to refer to papers and reports for results. Complete evaluation of the proposal would likely require review of partners’ proposals or statements of work. Furthermore, almost all accomplishments are models or studies that are under subcontract and in various stages of completion.

A major synthesis is needed that includes major results and data analyses. The synthesis should be prepared after the estuarine classification is completed (August 2011) and a monitoring design is fully developed, preferably at the end of 2011. The synthesis should be reviewed by the ISRP.

The proponents have accurately stated their commitment to adaptive management.

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

The proponents work cooperatively with numerous agencies and a university. As a major coordination/umbrella project, this project is very closely linked to many different ongoing projects in the region and this is well documented in the proposal. In particular it integrates with NOAA-Fisheries’ Columbia River Estuary ESA Recovery Plan Module for Salmon and Steelhead, MERR, and the Subbasin Plan.

The proponents have identified low dissolved oxygen, changing pH levels in the estuary in relation to offshore ocean processes, and climate change (increased temperature and changing precipitation patterns) as emerging factors that could affect estuarine ecosystems. The ISRP agreed these are important areas of near term or future studies.

Tracking fish via PIT tags installed by others is being done in collaboration with regional PIT tag database managers and is well coordinated. PIT tag detection in the estuary is a valuable new advance in technology.

This is clearly an RME project, but the proponents’ partners seem to be doing most of the reporting and publishing of the data from the project. A critical review of the reporting by primary authors and their affiliations should be included in the recommended synthesis.

4. Deliverables, Work Elements, Metrics, and Methods

The project has numerous important deliverables, including a classification system that will form the basis of a monitoring sampling design as well as specific projects to address estuarine habitat, food web structure, and salmon distribution and abundance.

As noted previously, the ISRP needs further details on methods and metrics to evaluate the scientific merit of this proposal. In several instances the information is given in cited documents (e.g., Roegner et al. 2008). More information is also required on document deliverables (reports, scientific papers) that give results of previous work.

This is a worthwhile project that promises to provide vital information necessary to recovery of estuarine habitats and improvement of estuarine survival of salmonids. However, the ISRP recommended one major qualification and concluded one particular task did not meet scientific review criteria, as follows: Qualification: The proponents should prepare a synthesis and integration of results (as mentioned in Objective 2, Deliverable 6), detailing major conclusions after the estuarine classification system is completed and a monitoring design is fully developed, preferably at the end of 2011. Preparation of this document should involve all the partners (NOAA, PNNL, Columbia Lands Trust, Columbia River Estuary Study Taskforce) and should also include methods and monitoring protocols from all subcontractors. The synthesis should be reviewed by the ISRP. In Part: Objective 1, Task 1 (g) - Does not meet review criteria “Evaluate the historic shift in base of salmon food web from macrodetrital to microdetrital sources and terrestrial versus marine derived organic matter sources.” A version of the proposal for this subproject was requested in the 2007/2009 project solicitation (200702600-Historic Changes in Organic Nutrient Sources and Productivity Proxies in the Columbia River Estuary in Relation to Juvenile Salmon Habitat Restoration Priorities). The ISRP concluded the project did not meet review criteria primarily because of weak application of the data to management actions, and this comment is still valid. 1. Purpose, Significance to Regional Programs, Technical Background, and Objectives The proposal is very significant to regional programs and describes a key project for implementation of the BiOp. The project is responsive to many regional programs/plans - 2008 BiOp (many RPAs), NOAA’s recovery plan for the estuary (Estuary Module, in press), MERR, and the NPCC Research Plan (regarding the overall estuary program). However, connections to estuary-wide goals of other agencies, such as the 16,000 acre restoration goal of EPA described at the September 2009 Astoria Science-Policy meeting, are not evident. 2. History: Accomplishments, Results, and Adaptive Management The project has a list of impressive accomplishments that should contribute significantly to improving understanding of estuarine ecology and serve as a basis for estuarine restoration efforts that should benefit salmon. Specific results were sometimes lacking, but this can be expected for a project of this scope. The proponents’ publication record can be improved; more documentation in the proposal is needed on results as the ISRP should not have to refer to papers and reports for results. Complete evaluation of the proposal would likely require review of partners’ proposals or statements of work. Furthermore, almost all accomplishments are models or studies that are under subcontract and in various stages of completion. A major synthesis is needed that includes major results and data analyses. The synthesis should be prepared after the estuarine classification is completed (August 2011) and a monitoring design is fully developed, preferably at the end of 2011. The synthesis should be reviewed by the ISRP. The proponents have accurately stated their commitment to adaptive management. 3. Project Relationships, Emerging Limiting Factors, and Tailored Questions for Type of Work (Hatchery, RME, Tagging) The proponents work cooperatively with numerous agencies and a university. As a major coordination/umbrella project, this project is very closely linked to many different ongoing projects in the region and this is well documented in the proposal. In particular it integrates with NOAA-Fisheries’ Columbia River Estuary ESA Recovery Plan Module for Salmon and Steelhead, MERR, and the Subbasin Plan. The proponents have identified low dissolved oxygen, changing pH levels in the estuary in relation to offshore ocean processes, and climate change (increased temperature and changing precipitation patterns) as emerging factors that could affect estuarine ecosystems. The ISRP agreed these are important areas of near term or future studies. Tracking fish via PIT tags installed by others is being done in collaboration with regional PIT tag database managers and is well coordinated. PIT tag detection in the estuary is a valuable new advance in technology. This is clearly an RME project, but the proponents’ partners seem to be doing most of the reporting and publishing of the data from the project. A critical review of the reporting by primary authors and their affiliations should be included in the recommended synthesis. 4. Deliverables, Work Elements, Metrics, and Methods The project has numerous important deliverables, including a classification system that will form the basis of a monitoring sampling design as well as specific projects to address estuarine habitat, food web structure, and salmon distribution and abundance. As noted previously, the ISRP needs further details on methods and metrics to evaluate the scientific merit of this proposal. In several instances the information is given in cited documents (e.g., Roegner et al. 2008). More information is also required on document deliverables (reports, scientific papers) that give results of previous work.

We look forward to working with BPA in providing clarification on our rotational panel design to support RPA 58.3 and in working with PNAMP on data management coordination to support RPA 72.

We also appreciate the opportunity to provide comments on the BiOp RM&E Workgroup determinations of 2008 BiOp RPA associations with our project. Our understanding is that the Workgroup determined that RPAs 56.1, 57.3, 58.2, 60.2, 71.1, 71.2 and 71.3 are not associated with this project. In addition, the Workgroup had questions about 58.3, 71.4, 72.1 and 72.3. We agree with the Workgroup determinations for the RPAs 56.1 and 57.3. Our responses to the remaining determinations are listed below:

 58.2     Develop an index and monitor and evaluate life history diversity of salmonid populations at representative locations in the estuary.

Response: This project fills data gaps needed to complete this RPA. We are collecting fish occurrence data, including salmon stock identification and species diversity, at all monitoring sites. Hence, the information collected under this project will be needed to fill spatial and/or temporal gaps, including habitat usage by salmonid stocks, needed to evaluate life history diversity. As an example, the salmon occurrence data collected under this project has been compiled and reported with AFEP project EST-P-10-New titled “The Contribution of Tidal Fluvial Habitats in the Columbia River Estuary to the Recovery of Diverse Salmon ESUs” by NMFS and UW. 

 58.3     Monitor and evaluate juvenile salmon growth rates and prey resources at representative locations in the estuary and plume.

Response: Our project directly implements this RPA.  We are collecting fish age (via otoliths) and prey availability and preference at all monitoring sites. The Estuary/Ocean RME Workgroup in June 2009 included this as a project associated with this RPA (see Attachment 7: https://www.pnnl.gov/main/publications/external/technical_reports/PNNL-18907.pdf).

 60.2     Evaluate the effects of selected individual habitat restoration actions at project sites relative to reference sites and evaluate post-restoration trajectories based on project-specific goals and objectives.

Response: This project is indirectly associated with this RPA. The focus of sites monitored under the Ecosystem Monitoring Program is relatively undisturbed emergent wetlands, or reference sites. To reduce costs in data collection efforts, there has been overlap in site locations and data collection for this project and our Reference Site project within our habitat restoration project #2003-011-00. Hence, the data from this project is used for comparison of restoration site action effectiveness data with reference sites.

We feel we are indirectly associated with the remaining RPAs 71.1, 71.2, 71.3, 72.1 and 72.3. These RPAs require participation and coordination with various regional efforts, such as AFEP, NPCC Fish and Wildlife Program and PNAMP. In some cases, we lead coordination activities in the estuary such as through annual estuary RME coordination meetings supported by the Ecosystem Monitoring Program funding that involve AFEP, state and NPCC/BPA-funded RME projects. In other cases, such as PNAMP workgroups, we are strong supporters and active participants, providing information and staff time.

 Thanks again for allowing us the opportunity to address these comments. Please feel free to contact us for further information or clarification on any of these responses.

The sponsors provided thorough responses to most of the ISRP's comments. They provided additional details to clarify most of the concerns the ISRP raised. It is gratifying to see a well thought-out approach to sampling the neglected freshwater tidal habitats of the Columbia River. The presentation of results related to contaminant monitoring in the lower Columbia River and estuary was especially well done. Of particular importance is the close cooperation of this project and Project # 200301000 "Historic Habitat Opportunities and Food-Web Linkages of Juvenile Salmon in the Columbia River Estuary and Their Implications for Managing River Flows and Restoring Estuarine Habitat." Both projects should benefit considerably from this collaboration.

Some concerns were not addressed very well by the sponsors, specifically those dealing with salmonid survival-habitat relationships and plans for publications. The sponsors adequately responded to the question of contaminant effects on survival, as the sponsors described models that would be used to forecast survival given body burdens and physiological limitations. A comparable response was not given on the relationship between survival and physical habitat/food supply.

It is unfortunate that this powerful team of researchers seems to be approaching the survival-habitat issue in oblique and indirect ways (through models, inference, etc) instead of trying to obtain some empirical data on juvenile salmonid survival in the Columbia River estuary. Perhaps the close cooperation with Project # 200301000 will help close the gap. Possibly, the current proposal could be refocused to increase critical mass on #200301000. Survival in relation to habitat factors is notoriously difficult to assess in estuaries, and a large team with good funding is required to make progress, especially in large systems like the Columbia River estuary.

The proponents make the statement, "The Ecosystem Monitoring Project is an ongoing monitoring project in the lower Columbia River and estuary whose goals are to create a consistent approach to protocol development and status and trends monitoring of estuarine habitats." In reality, therefore, the Project is really a research program to develop monitoring tools. The real monitoring program is yet to be set up.

Although a substantial amount of work has been completed, some tasks defined in the original proposal are still in progress (see pages 19-21 of the sponsor's response). A major concern is that delays in completion of the tasks in the original proposal would set back completion of the work proposed for 2007-2009. Completion of some of these tasks is apparently contingent on finalization of the Lower Columbia River and Estuary Ecosystem Classification System. New technologies and approaches will always arise that allow refinement of the habitat classification system, but the classification is so crucial to the habitat work that it should be completed as expeditiously as possible and submitted for peer review in the early stages of the project.

Qualification: The sponsors should finalize the classification system as soon as possible so that it can used to complete the tasks contingent upon it.