The response failed to fully address several of the major concerns raised in the original ISRP review. The four, primary concerns expressed in the original review were:

1. Provide a synthesis and model of the existing data as justification and guidance for prioritizing project activities and identify the most promising future projects.
2. Specify the RM&E and adaptive management plans in sufficient detail for ISRP review.
3. Further detail is required on the staging of the various components of restoration.
4. The ISRP requested clarification on the relationships and coordination among the various restoration projects that are being implemented on this stretch of the Kootenai River.

The ISRP concerns about the staging of various components of this project were partially addressed. The text and tables included in the response to clarify scheduling were helpful. The inclusion of the Gantt chart that was requested in the original ISRP review did not help because it was unreadable. The sponsor indicated that the lack of clarity in their description of the sequencing of project activities in the original proposal was largely due to the structure of the Objectives section of the proposal form. Although the form may be cumbersome, many of the other projects reviewed by the ISRP were able to clearly convey scheduling of project activities. Although the response partially addressed the ISRP concern on this issue, the sequencing of objectives and work elements presented is still confusing.

Administrative relationships among the Kootenai River projects were adequately described in the response. However, technical relationships among the various projects were not described. This problem was common to all the Kootenai River proposals. For that reason, the ISRP suggests that a synthesis report be produced summarizing the results that have been obtained from the RM&E efforts associated with these projects. The synthesis should not be a simple tabulation of data collected but a concise and comprehensive interpretation 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 (ISRP 2012-3).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.

A link to the draft Adaptive Management Plan (AMP) was provided with the response. Although still under development, this plan does indicate the types of information that will be used to assess project effectiveness and provides a process by which this information will be used to modify future restoration efforts and monitoring plans. However, some vital elements of an adaptive management process appear to be missing. For example, how experimentation will be structured in a manner that will inform decisions and how management decisions will be made are not described.

The relationship between the subbasin AMP and the monitoring planned for the reconnect projects is not clear. The response includes a lengthy description of various biotic indices used to track biological response to project implementation. These indices are not explicitly addressed in the subbasin AMP plan, leaving it unclear as to how the monitoring of the reconnect projects will be integrated into the subbasin AMP process.

The biotic indices are a useful mechanism for assessing biological response to the reconnect projects. However, without accompanying information on changes in physical and chemical habitat attributes, it may be very difficult to ascribe a cause to an observed change in an index. Ideally, an RM&E plan would be developed that couples these indices with assessment of water chemistry, physical habitat conditions, and trophic relationships. The process to be used for data storage and retention was fully explained and appears well designed.

A dynamic ecosystem model (e.g., Ecopath) would also help the sponsors address their goal of “creating conditions that help support and enhance the food web” of the Kootenai River. Use of such a model would help link the reconnect project to efforts on the mainstem of the river and provide insight into how this project will support the overarching objective for the Kootenai River Habitat Restoration Plan (KRHRP), which seems to be “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” (from proposal project 200200200). Such a model would be useful in the context of the Operational Loss activities as well.

The response to the ISRP concern that climate change was not being adequately considered was not sufficient, and the response about invasive species was incomplete. The response to this issue creates the impression that climate change has not been seriously considered in the design of the restoration strategy for the Kootenai River and its floodplain. Further,description of procedures to monitor the spread of Didymo was complete but there was no discussion of measures being implemented to address other invasive species.

The ISRP request to see a more thorough explanation of how the baseline information was used to inform the design of the Ball Creek project was not fully addressed. The original proposal and the response indicated that considerable effort had been devoted to collect information on characteristics of the Ball Creek project site prior to designing the reconnection project. The ISRP desired some discussion of how this baseline information influenced the design of the restoration plan. The information provided only superficially addressed this point.

Despite the remaining deficiencies in the proposal, Objective 1 (continue with the Ball Creek reconnection) has progressed to the point where implementation seems appropriate. In addition, the approach proposed for Objective 3 (restoration ranking plan) appears to be technically justified. However, the adequacy of the approach for Objective 2, the design and implementation of future reconnect projects, cannot be assessed from the information provided. The prioritization process for identifying future projects (Objective 3) needs to be completed and specific future project sites identified before components of the project related to Objective 2 can be reviewed. It seems premature to include funding for future restoration project design and implementation until sites are identified and some understanding of the nature and extent of the work required is determined.

Responses requested:

1. Further detail is required on the staging of the various components of restoration.
2. Specify the RM&E and adaptive management plans in sufficient detail for ISRP review.
3. Provide a synthesis and model of the existing data as justification and guidance for prioritizing project activities

This project is addressing an important habitat deficiency in the project area. However, the proposal was poorly organized, making it difficult to understand how activities were to be sequenced and the extent to which proposed actions were founded on previously collected data. There was no indication that data previously collected has been synthesized to any appreciable extent or used in a formal manner, statistical or otherwise, to guide development of project activities. Further detail is required on the staging of the various components of restoration. A flow chart or Gantt diagram would be very useful in this regard. The field visit in October provided insights into the complexities being faced by the sponsors, but these were not adequately reflected in the proposal.

RME and adaptive management components of the plan are incompletely described. The sponsors indicate that these topics are to be addressed in two documents that are currently being developed. RME and adaptive management are critical components of any restoration effort and a complete technical review of this project would require that these two plans be included with the proposal. At a minimum, the subbasin adaptive management plan should be included with the response to this ISRP review.

The ISRP requests a revised proposal that emphasizes synthesis and modeling of the existing data as justification and guidance for ecosystem scale restoration activities and that focuses on the priority activities needed to make the floodplain functional once again. This project has tremendous potential, not only locally in terms of restoring fish and wildlife, but also as a demonstration to the broader restoration community as to what is possible. Unfortunately, the present proposal will not achieve that potential.

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

Restoration of riparian wetlands along this reach of the Kootenai River would be significant to regional ecological restoration. Almost all listed species will potentially benefit from floodplain reconnection. As an example the Meander Reach of the Kootenai River, where this project will occur, is listed as critical bull trout habitat in the 2006 BiOp.

The proposal clearly defines the historic extent and biological productivity of wetlands along the Kootenai River in Idaho and the extent to which floodplain habitat in this region has been reduced. The authors seem quite familiar with the literature on the subject matter and adequately describe the impacts of the operation of Libby Dam and altered land use on ecological processes of the study reach. The technical background provides a fairly good description of the problem and relies heavily on the Operational Loss Assessment results. It would have been helpful to provide a link to the Operational Loss Assessment as this document did provide useful information, especially for showing the changes in trophic structure along the various reaches. For example, the ISRP also found a useful presentation of the Loss Assessment at www.powershow.com/view/14ff6e-YjI1Y/Floodplain_Operational_Loss_
Assessment_on_the_Kootenai_River_Watershed_Downstream_from_Libby_Dam_flash_ppt_presentation. One issue that was not adequately discussed in the proposal was the extent to which flows from Libby Dam could be manipulated to encourage more channel-floodplain interaction. 

There appears to be some discrepancy between the objectives of this project and the assumptions on which other proposed projects on the Kootenai River are based. The sponsors state, “The project was originally designed to improve conditions for larval and juvenile rearing of Kootenai sturgeon and positively affect sturgeon recovery by restoring natural ecosystem functions. The project was funded to locate a site and evaluate its suitability for reconnecting the river and floodplain (Scott and Clayton 2004). The objective of this initial phase was to find a site that would provide low-velocity, off-channel refugia for juvenile sturgeon and stimulate ecological function by expanding floodplain habitats and associated trophic productivity.” The Kootenai proposal that is focused on ecosystem restoration for sturgeon is based on the assumption that recruitment at the larval stage is a bottleneck, not survival of the juvenile stage, which would likely use off channel habitat provided by this project. Riparian wetland restoration is still a worthwhile objective. But the benefits for sturgeon presumed from this project should be consistent with the assumptions in the other proposals.

A significant problem with the objectives is that there is no guiding model(s) based on previous data to prioritize the research and restoration efforts. A substantial amount of work has already been done, but it is not informing the next restoration phase in a logical and quantifiable manner. Thesupporting text for each objective is often inadequate. For example, OBJ-3 seeks to implement invasive species control management techniques in floodplain habitats (a general objective) by 2015, but only Reed canarygrass is targeted (very specific). This objective also suggests the assumption that natural communities will outcompete Reed canary grass if native vegetation is introduced on a site. Generally this is not the case until habitat conditions that discourage reed canarygrass such as flooding frequency are sufficiently restored. In some cases, even the restoration of habitat conditions appropriate for native species may not be sufficient to enable suppress canarygrass, and ongoing site maintenance may be required. OBJ-2 seeks to implement floodplain reconnection activities in conjunction with BPA mitigation projects 199206105 and mitigation phase of 200201100 by 2021 but the text only addresses strengthening the Tribal Fish and Wildlife Program’s ability to share resources, information, and reduce duplication and costs in floodplain ecosystem restoration. Other objectives share these problems.

The reality is that the river is fundamentally different now than prior to European settlement and construction of Libby Dam. A new system has emerged, one that is not well connected to the historic floodplain ecosystem, and restoration of previous functionality requires thinking in new ways and on new scales. The proposal does not fully communicate an understanding of how this project will be linked to ecosystem responses at broader scales. While there are lots of activities taking place there is a notable lack of synthesis both in working models and in peer review publications.

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

The history of this project is thoroughly described in the proposal. The project sponsors have conducted baseline research and monitoring to understand the nutrient dynamics within lotic and lentic systems on the Kootenai river floodplain and using this information formulate the hypothesis that wetland restoration may increase nutrient delivery to the river and stimulate primary and secondary productivity. The ISRP identified several issues related to the interpretation of the baseline information:

1. The trophic analyses are quite limited as there is no mention of decomposition, organic matter dynamics, or microbial food webs.
   
   
2. The low chlorophyll a levels in water samples from lotic systems was interpreted as an indication of low primary productivity in these systems relative to lentic habitats. However, most primary production in small, flowing systems is supported by periphyton, algae attached to the streambed substrate, rather than from phytoplankton in the water column. Phytoplankton is more prevalent in lotic habitats. Therefore, the contrast in chlorophyll a levels between these habitat types may be an artifact of the sampling methods rather than an actual disparity in primary production. 
   
   
3. The sponsors state (p.13) “In addition to nutrient sampling, we collected samples that represented primary producing organisms (chlorophyll a and phytoplankton taxonomy) as well as primary producing organisms (zooplankton).” Please note, zooplankton are secondary producers.
   
   
4. The proposal also states “The graphs shown in Figure 20 suggest that the increased primary production (chlorophyll a) in the lentic areas might reflect the increased nitrogen (DIN) available,” but earlier they state that data were not sufficient for statistical analyses (note lack of error bars on Fig 20).

Despite these issues with data interpretation and analysis, the conclusion that increasing the presence of riparian wetlands would be of benefit to the ecological health of the ecosystem is still valid. But it will be important to ensure that deficiencies in sampling and data analysis are addressed in RME efforts designed to evaluate the effectiveness of the Ball Creek wetland restoration project and other floodplain reconnection projects in the meander reach. 

The adaptive management effort associated with this project was not adequately described in the proposal. The project appears to have some form of an adaptive learning process but the proposal does not clearly describe the structure of this process. Is there an effective mechanism for transferring RME information to decision makers? Is there a formal process for using this information to make project management decisions? How are decisions made and who makes them? The proposal does indicate that a subbasin-scale adaptive management plan is under development, and this plan will guide adaptive management efforts for all habitat restoration efforts in the project area. Presumably, these questions will be addressed in the plan. However, the adequacy of the adaptive management process for this project cannot be assessed unless this plan is a component of the proposal.

ISRP Retrospective Evaluation of Results

The results of research conducted to date in support of this project are described in the proposal, as noted above. However, it is not clear that this information has been used to full advantage. At least three key activities are missing that are essential for success: hypothesis testing, model development, and serious periodic information syntheses. Substantial information is being acquired about the system, but it is not being effectively translated into knowledge or actions that will do more than provide incremental benefits to fish and wildlife.

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

The relationship of this project to other efforts ongoing in the same area was not fully described. In particular, there seems to be considerable overlap in project objectives between this project and the large habitat restoration program proposed for this reach of the Kootenai River (200200200 - Restore Natural Recruitment of Kootenai River White Sturgeon). The project reviewed here provides details for a specific project, the restoration of Ball Creek and associated wetlands, while the other proposal for "Restore Natural Recruitment of Kootenai River White Sturgeon" describes a large habitat restoration program that will identify and implement a variety of projects over time, including the restoration or riparian wetlands. Both this proposal and the one for the restoration program should have clearly indicated why these proposals are separate and how efforts between these two projects are being coordinated. The relationship between these proposals was only very briefly discussed. This proposal also indicates that there has been an ongoing study of nutrient dynamics in the project reach, yet no results from this effort are presented in the proposal. It would seem, given that one of the key objectives of the Ball Creek wetland restoration is to increase nutrient delivery to the Kootenai River, that these efforts would be closely coordinated. But the relationship between these projects is only briefly discussed.

The project does indicate that they will utilize hydrologic models to predict possible impacts of climate change on project effectiveness.Potential changes in winter ice conditions due to climate change or alterations in winter flow conditions were not discussed. Icing is a major driver of ecological processes in streams and shallow water areas, and winter icing conditions are influenced by alterations to temperature, cloudiness, vegetation, and water flows. There is no mention of possible impacts for increasing human population or alteration of land use over time. Also, the potential impact of invasive species, other that Reed canarygrass, was not addressed. Given that Didymo does occur in the system and that there are a number of other aquatic species whose introduction could affect project success, this factor should be considered.

4. Deliverables, Work Elements, Metrics, and Methods

While it is refreshing to see the project taking an ecosystem approach to floodplain restoration, it is important to proceed in a logical and thoughtful manner. Unfortunately, it appears from the long list of deliverables that the sponsors are trying to do everything at once. Further, there are deliverables that overlap as well as deliverables that should have been completed as part of previous projects or as part of the proposal preparation process. For example, CR1-4 (Literature review and study design analysis of critical uncertainties research) and CR3-4 (Sampling and laboratory analysis protocol development) should have been completed and used in the development of this proposal. Similarly, P&C2-5 (2D floodplain inundation hydrologic modeling and USGS ground/surface water review), a review and analysis of the 2D floodplain hydrologic modeling efforts for project 200201100, should have been completed, and the results used to develop this proposal. Most importantly, there are no priorities for the deliverables. The Deliverables aspect of the proposal needs to be revised and consolidated to show deliverables as part of an integrated research/ restoration effort. One or more deliverables should focus on a major synthesis (to be peer-reviewed) and the development of a quantitative ecosystem model(s).

The work elements proposed for this project are quite detailed but poorly organized. As a result, it was difficult to relate work elements with their associated deliverables and objectives. The manner in which the work elements were presented also made it difficult to envision how the project is intended to be sequenced. Three work elements: IV1-3: Literature review for invasive species control management techniques; IV2-3: Experimental design for invasive species control management techniques; IV3-3: Implement invasive species control management techniques, could benefit from review of the invasive species control work described in the ISAB Invasive Species Report and ISRP Wildlife Reviews.

There is a lack of detail on the RME effort that will evaluate project effectiveness. The proposal indicates that a subbasin scale adaptive management plan is under development and that RME will be comprehensively described in this document. Only a very general description of the monitoring goals, design, and protocols is provided in the proposal. This adaptive management plan should be included with the response to the ISRP comments. Technical evaluation of the RME and adaptive management components of this proposal are not possible without this plan.

There was inadequate discussion of data management in the proposal. Data management and retention protocols are critical for an RME effort, especially for large projects like those planned for the Kootenai River and its floodplain. There also is a concern about the data management being off-site, but perhaps that will be appropriate over the longer term as data management becomes increasingly complex. The ISRP hopes this issue will be thoroughly addressed in the subbasin adaptive management plan. As noted above, this plan needs to be included as a component of a revised proposal to enable ISRP review of RME and adaptive management associated with the suite of Kootenai River projects.

As a general comment, substantial data has been collected for this project already, but little predictive understanding seems to be emerging. Basically the group is drowning in unassessed data without fully using it to generate knowledge. More emphasis should be placed on generating syntheses from these data. Application of predictive models and rigorous use of testable hypotheses/relationships in developing syntheses will help generate information useful for informing managers and guiding future RME efforts.

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

The general outline of the RME process to be used in assessing the Ball Creek wetland restoration project is very brief. A link was provided to website that was supposed to provide additional detail on the sampling methods to be employed. The descriptions of many of the methods at this site were not complete and, therefore, could not be adequately evaluated.

Some of the methods that were briefly described in the proposal did raise questions. The sponsors state, “From its inception, the Reconnect Project built in a Research, Monitoring and Evaluation (RM&E) component that estimates trophic level responses to proposed restoration of floodplain and ecosystem function. Subbasin-wide monitoring will provide a long-term baseline, plus feed back into the overall Index of Ecological Integrity (IEI), developed by the Kootenai River Floodplain Ecosystem Operational Loss Assessment Project (BPA 200201100), to capture the contributions of each project and the cumulative effects of multiple projects to the IEI.” However, the IEI appears to be a very simplistic and preliminary method of aggregating effects. The sponsors want to develop a trophic model which will apparently supersede the IEI. More information is required on the proposed model. The proposal also mentions a fish index, but methods for sampling fish or specifics about the index are not given. Are fish assessment protocols aligned with those to be used in project 199806500, Kootenai River Fishery Investigations?