Responses to each of the three ISRP requests were well reasoned, well written, well referenced and generally compelling given the information available. The response satisfactorily addressed the bulk of the ISRP concerns.

The American River culverts were adequately described. Estimates of American River discharge when adult steelhead were expected to migrate into the stream (mid-April through May) were shown. FishXing software was used to estimate the percentage of time adult steelhead could pass through the existing culverts and enter the American River. The FishXing model runs suggested that a flow greater than 248 cfs through the culverts would block passage by adult steelhead. Table 1 indicates that 64% of the daily discharge rates from mid-April through May during the years 2007-2012 exceeded 248 cfs. In some years (e.g. 2007, 2010, 2011, and 2012) flows exceeding 248 cfs occurred over multiple consecutive days. The assumptions used to estimate stream flow and swimming capacity of adult steelhead were based on available information and were clearly articulated. If they are correct, the existing culverts represent a passage barrier for steelhead adults at flow rates that commonly occur during the spawning migration period. A similar analysis was not done for adult spring Chinook. Such an analysis would have been informative because the arrival dates and swimming capability of this species may differ from steelhead. Additionally, it is stated that the American River could act as a refuge during the summer due to its generally cooler waters and also serve as an overwintering location for salmonids. During these time periods flows would likely be at base levels or slightly higher. It would be useful to perform FishXing model runs at these times of year for juveniles to see if flow and waterfall conditions at the culverts are potentially blocking these fish as well. Results from such modeling efforts would further delineate the effects of the existing culverts on salmonids and other fishes.

Limited stream habitat surveys plus water quality data and stream gradient information were used to estimate the amount of steelhead and spring Chinook spawning and rearing area potentially available in the American River drainage. A figure showing the distribution of these areas in the watershed was provided. The sponsors estimate that about 53 stream miles of spring Chinook and 76 stream miles of steelhead spawning and rearing habitat would be available if passage at the culvert site were improved. Again the assumptions behind these estimates were clearly presented and appear to be reasonable given the current state of knowledge.

Installing a pre-cast concrete arch having a 40 to 50 foot opening with a natural stream bottom is being proposed to alleviate the fish passage problems at the culverts. A bridge and placing baffles in the existing culverts were the alternatives that were considered. The bridge option was rejected because of cost considerations. The use of baffles in the culverts was also overruled because of potential debris buildup and possible culvert failure during high flow events. The sponsors are seeking additional funding from NOAA Fisheries to purchase and locate the concrete arch.

Regarding Crooked River, the response gives additional justification for expecting substantial benefits to fish. The sponsors maintain that significant biological benefits for juvenile fish will be created by the project. Cobble embeddedness is expected to be significantly improved by restoring hydrologic functions. For example, fines will be deposited in reconnected floodplain areas or flushed out of the river. This reduction in cobble embeddedness should improve food production and enhance spawning areas. Additionally, large woody debris will be added to the restored stream to provide cover for juvenile salmonids. Currently stream temperatures during summer months can reach lethal levels for salmonids. Reconnecting hill slope groundwater sources to the main channel, reducing stream width to depth ratios and planting in riparian areas is expected to ameliorate temperature impacts. A significant amount of floodplain area will also be reconnected to the Crooked River.

None of the potential biological benefits originating from these changes, however, can be realized without fish. Recently 350 to 800 HOR and NOR adult Chinook salmon have returned to the Crooked River. Experimental design constraints imposed by the ISS kept HOR adults from being released into the Crooked River. Those restrictions were ended in 2012, opening the river up to both HOR and NOR adult Chinook salmon. Additionally, 400,000 juvenile steelhead and 400,000 juvenile Chinook are annually released into the Crooked River. It is expected that these fish will benefit from the effects of the planned restoration of the Crooked River.

Two unpatented mining claims do exist in the Crooked River. The sponsors state that there are no plans to activate these claims. Additionally, they assert and that the high cost of a required habitat restoration bond imposed on claimants will prevent the mines from being developed.

The sponsors plan on using AEM to assess whether anadromous fish production has increased in the Crooked and American Rivers. They will use changes in habitat features, counts of adults and emigrating smolts as well as changes in smolt size in their analyses. In the Crooked River, NOAA Fisheries researchers will be developing an AEM plan specific to that project. Past data from a screw trap located close to the mouth of the American River plus historical redd counts within the watershed will be compared to information obtained after restoration to help evaluate how restoration actions in this basin may have influenced salmonid abundance and productivity. The sponsors need to indicate the statistical approaches, e.g., BA, BACI designs, they plan to employ with these data.

Evaluation of Results

This is a relatively new project, but some work has occurred in both the Crooked and American River basins. Three miles of roads were decommissioned in the American River watershed and approximately 6 acres were treated for weeds in the Crooked River in preparation for a riparian planting. Inventories of existing culverts, bridges, and roads were completed in the American River and started in the Crooked River. Starting in 2012, a project using LiDAR, GPS surveying, and other information was used to create a restoration design for the highly altered lower portion of the Crooked River. Another design study examined alternative locations for three miles of the “Narrows Road” which is situated in the floodplain of the Crooked River.

There are two qualifications regarding the American River component of the project and one regarding both the Crooked River and the American River component. All should be resolved during contracting. The two Clearwater Programmatic Comments also apply.

For the American River, FishXing model runs were performed to estimate the effects of two existing culverts on the ability of adult steelhead to migrate into the American River under different flow conditions. Similar runs for adult spring Chinook and juvenile salmonids should also be performed to further delineate the potential impact these structures play on access to the American River at different times of the year and on different salmonid species.

The response does not refer to any information from the Idaho Supplementation Study (ISS) or from any steelhead or Chinook tagging/marking/tracking that might have been done in the past that either supports or calls into question the assumption that the American River culverts are impeding fish movement. If any information exists it should be incorporated into the feasibility analysis.

The sponsors need to indicate the statistical approaches, e.g., BA, BACI designs, that they plan to use to measure hypothesized increases in anadromous fish productivity and production generated by their restoration actions. Success in achieving Objective 7 (increase anadromous fish productivity and production) will be difficult or impossible to demonstrate if "fish in - fish out" monitoring by IDFG were to be discontinued before 2018. Regional coordination is needed to assure effective monitoring.

A response is requested regarding three items:

1) Further analysis is required to determine how much of a barrier the American River culvert(s) is to fish. More information is needed to justify this substantial culvert project (DELV 5). Refer to comments in section 4 below.

2) The proposed reconstruction of the lower 2 miles of Crooked River (DELV 6) will provide a more functioning watershed, but will the overall fish benefits be enough to demonstrate the effectiveness? Are anticipated returns of fish adequate to justify this kind of effort? What is the status of the mining claim?

3) Explain how success in achieving Objective 7, “increase anadromous fish productivity and production” would be measured. This is a strong proposal in some regards, but results should be judged in terms of improvements to fish productivity and production.

See the programmatic comments on the Clearwater projects.

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

This proposal is designed to address the limiting factors that were identified in the Crooked and American Rivers by the 2012 FCRPS BiOp Expert Panel process. Dredge mining and road development significantly impacted these two upper tributaries to the South Fork Clearwater River. Particularly helpful for this review were the concise summaries of the population units being targeted, their status, and their relationship to MPG and ESU viability assessments.

The South Fork Clearwater Landscape Assessment and the Nez Perce Forest Plan state that the South Fork Clearwater and its upper tributaries, the Red River, Newsome Creek, and Crooked and American Rivers have the potential to be important areas of steelhead and spring Chinook production after restoration. Restoration work is occurring in Newsome Creek and in the Red River basin. Addressing habitat limitations in the American and Crooked Rivers is of regional significance as successful restoration of these systems will help increase the abundance and persistence of summer steelhead, spring Chinook, Bull trout, and possibly Pacific Lamprey.

The project has nine objectives. They include increasing fish abundance and productivity; improving habitat diversity and complexity; reducing stream temperatures, the presence of fish passage barriers, sedimentation, and the occurrence of noxious weeds; restoring historic wetlands; and protecting riparian habitats and existing critical habitats that are under the threat of development. All of the objectives have success criteria, which is laudable. Some however, need further refinement or explanation. Two measures, an increase in egg-to-smolt survival and an increase in smolt size will be used to measure improvements in fish abundance and productivity. At some point, density dependence effects will reduce smolt size and density dependence may also induce migration from the project area which could disguise survival increases. How will these possible outcomes be taken into account, could other metrics be employed? The objective associated with protecting and restoring riparian habitats has a success criterion of creating a plant community with a 75% or greater species similarity to the natural community. No mention, however, is made of any plant density objective, for example, so many willows per ten square meters of habitat. The wetland restoration objective is not clearly stated, it appears that only historical or identified wetlands that are 5 or more acres will be restored. What was the rationale behind the 5 acre rule?

The overall description of the proposed monitoring plan (page 12) is well organized and helpful, but seems misplaced; it should be under RM&E.

Four objectives require further refinement or clarification. The "success criteria" listed for Objective 1 are not success criteria in the sense of those developed more appropriately for other objectives; instead they are metrics such as linear feet of treatments specific to the proposed reconstruction of lower Crooked River. They should be labeled as such. Objective 7, to increase fish production, should be the overall stated purpose of the project. A critical deficiency is that the proposal does not include provisions, or at least a description of such provisions, for measuring success in achieving Objective 7 (increase anadromous fish productivity and production).

For Objective 4, a success criterion is "to meet a < 20 percent cobble embeddedness metric for the watershed.” This metric is vague and should include what particle size and where to be assessed. Reviewers challenge sponsors to become actively engaged in the details of sediment-fish survival relationships including recent studies and to work toward better connecting physical habitat in Crooked and American rivers to anadromous fish.

Similarly, Objective 3 is to reduce stream temperature to specific criteria. It seems time for the sponsors to think in terms of temperature goals that are specifically tied to dealing with limiting factors for a specific life stage of a specific fish species in a specific stream reach. That would entail knowledge of current habitat use and an understanding of how close a given physical attribute in each reach (say temperature) is toward not being a limiting factor. Then assess how to maximize the return for a range of possible restoration actions and choose the best.

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

Even though this is a new project some work has occurred in both the Crooked and American River basins. For example, 2.9 miles of roads were decommissioned in the American River Watershed and approximately 6 acres were treated for weeds in the Crooked River in preparation for a riparian planting project that will occur in 2013. Inventories of existing culverts, bridges, and roads were completed in the American River and started in the Crooked River. The lower two miles of the Crooked River were significantly altered by dredge mining. Starting in 2012, a project using LiDAR, GPS surveying, and other information was used to create a restoration design for this portion of the Crooked River. Another design study in the Crooked River examined alternative locations for three miles of the “Narrows Road” which is situated in the floodplain of the Crooked River. The costs and benefits of four alternative routes were assessed and a preferred route was determined.

Because the project is new, few opportunities have existed for adaptive management. However, the aforementioned Narrows Road project is an example of how data may be used to reshape restoration activities. Originally, the plan was to move the road completely out of the 100-year floodplain and place it on the surrounding hillside or alternatively to use an existing road to access the watershed from a different location. A feasibility analysis showed both of these choices would be prohibitively expensive. This caused the sponsors to modify their preferred choice; the final alternative now has relocated the majority of the road out of the 50-year flood zone. The sponsors state that they will alter or change restoration actions when new information points them to more effective procedures or methods.

This proposal demonstrates that advice from the ISRP's review in 2006 has been taken seriously as the monitoring and adaptive management components of the proposal are much improved. However, the description of adaptive management refers to a “passive” approach. The ISAB (see ISAB 2011-4) and ISRP promote active adaptive management, consistent with the original definition of the term, in which experimentation is deliberate in order to reduce key uncertainties, with the goal of improving future decisions. This approach places a value on knowledge to reduce uncertainty in the future, as an outcome in itself, and requires formulation of alternative hypotheses and an experimental design to test those hypotheses.

The description of proposed monitoring under the “Problem Statement” and “Monitoring” (as DELV-13) is generally good. The main deficiency is that the proposal does not include provisions, or at least a description of such provisions, for measuring success in achieving Objective 7 (increase anadromous fish productivity and production).

3. Project Relationships, Emerging Limiting Factors, and Tailored Questions

U.S. Forest Service personnel stationed in the Nez Perce Clearwater National Forest are important partners in this project. Personnel, resources, and equipment from the Restore and Protect Red River Watershed, Restoration of Newsome Creek, and Lower South Fork Clearwater River Watershed Restoration projects are being shared with this project. All of these projects are led by the Nez Perce Tribe. Other ongoing studies that complement the American and Crooked River project are the Nez Perce Tribal Hatchery Monitoring and Evaluation, Red River Meadow Restoration (IDFG), and the B-run steelhead Supplementation Effectiveness Research projects. Coordination with the Bureau of Land Management, Idaho County Highway District, and Idaho Department of Transportation will also occur as projects are implemented. The sponsors worked with the River Design Group to create a restoration plan for a portion of the Crooked River. Currently they are working with NOAA-Fisheries researchers to develop a monitoring and evaluation plan for the Crooked River project.

Climate change, invasive species, and toxics were mentioned as possible emerging limiting factors. The possible effects of climate change are influencing proposed restoration actions. For instance, all bridge crossings and culverts are being designed to withstand 100-year floods. Removing fish migration barriers, restoring riparian vegetation, and reconnecting floodplains to their rivers were all given high priorities. These actions are expected to reduce stream temperatures or in the case of passage improvements provide fish with potential cool water refugia. Procedures for invasive weed control have been established. Brook trout are regarded as an invasive species. Their possible colonization of newly opened habitat is considered when fish passage barriers are being prioritized. Scans for heavy metals in the project area occurred in the 1980s, 1990s, and again in 2010 to see if mining activities had left contaminants. These surveys found that heavy metal concentrations did not exceed expected background levels.

4. Deliverables, Work Elements, Metrics, and Methods

The project has fifteen deliverables. Ten are for specific restoration actions, six of these will occur in the American River, and four of the six are being conducted to improve fish passage. One of the remaining two American River deliverables is for planting trees in a riparian zone adjacent to a part of the stream that had undergone some restoration by the BLM. The remaining deliverable is a place holder for funds to purchase or obtain an easement on the Maines Estate. Prime rearing and spawning areas in the American River exist on the property which may be sold and developed unless the sponsors can negotiate an alternative arrangement with the owners. Four restoration actions will occur in the Crooked River. Two of these are linked to a planned restoration of 2 miles of the stream. One of these is for actual restoration while the other one is for the development of a monitoring and evaluation plan specifically for this restoration action. The other two Crooked River deliverables are for fish passage and road modifications. Three other deliverables (project management, inventories of stream habitat, and weed control) are for activities that will occur in both rivers.

The project has two very significant deliverables that are major efforts. One (DELV 5) is at the mouth of the American River where it is being proposed that two culverts be removed and replaced with a pre-cast concrete arch having a 40 to 50 foot opening with a natural stream bottom. More information about the size of culverts and stream flow information is needed to justify their replacement. A photograph of the culverts was provided, and it appears that they may be 12 feet in diameter, have corrugated bottoms and are undercutting the stream. The sponsors are seeking additional funds from NOAA to design and implement this replacement.

The proposal makes the sweeping assertions that the "barrier at the mouth of American River was identified as a barrier to adult steelhead at high flows and a barrier to juvenile steelhead and Chinook salmon at most flows" and "Replacing this culvert will provide access to around 100 miles of stream habitat at all flows." The statement that access would be provided to 100 miles of habitat at all flows seems doubtful because at some flows there is likely very little fish movement. Unfortunately, the tour did not visit the site. From the photo it appears dubious that this would be the barrier of the magnitude depicted. Justification of the assertions is needed, including a summary of FishX modeling results, a summary of current anadromous fish use, and a discussion of realistic gains if it was replaced. Also, discussion of those alternatives including modifications to existing structures that were considered should be presented, with the rationale behind rejection of each.

The second significant deliverable is DELV 6, the restoration of 2 miles of the Crooked River that had been severely impacted by dredge mining. Mining operations artificially increased the number of stream meanders, denuded the riparian zone, channelized the river, and reduced the floodplain. The sponsors have already worked with a subcontractor, the River Design Group, to develop a restoration plan. They are also working with P. Roni and colleagues at NOAA to develop an Action Effectiveness Monitoring Plan specifically for this restoration action. Like the American River culvert replacement project, additional funds from NOAA are being sought to implement this project.

Although the sponsors state that action effectiveness and status and trends monitoring will be performed, it is unclear what types of before treatment data might be available. It is mentioned that the U.S. Forest Service, BLM and IDFG are collecting data. Having a brief summary of the types of information collected and how it might be used to help appraise the impacts of the restoration actions proposed here would have been a helpful addition to this proposal.

Again, no deliverables are listed in relation to Objective 7, increase anadromous fish productivity and production. No description of monitoring to measure progress toward objective 7 is provided.

Modified by Dal Marsters on 9/27/2013 11:26:03 AM.

The sponsors provided brief and general answers to ISRP comments, rather than addressing the comments in the level of detail that was expected. The ISRP requested "greater and clearer detail of the specific activities to be undertaken." It also stated that "the proposal would benefit from a more clearly identifiable need and justification for its undertaking relative to objectives (measurable), benefits to focal species (salmon and steelhead), and effects on non-focal species..." The sponsor's response was simply to insist, "The proposal narrative gives a very specific description of work to be completed during this funding cycle."

The sponsors appear to have misinterpreted the ISRP's original review comment pertaining to justification for this project's elements (including barrier removal). The ISRP does not dispute the general idea that removal of barriers can - but not necessarily will - result in increased fish production. As a fundamental and general principle this has support and documentation. Rather, the ISRP sought justification of each project based on the quality and quantity of habitat above a barrier (not just miles of stream as the sponsors propose) and the potential increase in fish use and benefit. The ISRP recommends as a precursor to barrier removal (perhaps as a future stand alone project) a quantitative evaluation of habitat quality and quantity above each barrier, and that these estimates should play a major role in prioritizing barrier replacement/removal projects. Provisions also should be made for some level of assessment of fish use and abundance after barrier replacement/removal.

The ISRP requested more detail on criteria for selecting roads that were to be decommissioned or improved. The sponsors did not provide this information, but rather the response was "The Nez Perce Tribe's Fisheries Watershed Department focuses solely on watershed restoration. Roads identified for improvement or decommissioning are truly focused on reducing chronic sediment input into streams for habitat improvement."

The ISRP requested that the proposal ..."needs measurable objectives specified in terms or biological response..." The sponsors responded that it is "...extremely difficult to provide direct ties to numbers of fish or wildlife..." without providing any additional details about why it is difficult or suggesting how biological responses would be assessed. The ISRP requested that the discussion of M&E needed to be expanded. The sponsors stated, essentially, that funding was not sufficient to allow data collection to show compliance and effectiveness. This response is perplexing in that the sponsors proposed to collect physical habitat and biological data in the original proposal. This data should provide insight into project effectiveness, but the sponsor's response raises questions about whether the data will be analyzed.

In short, the ISRP knows little more about this project than was provided in the original proposal. ISRP comments similar to those addressed to the sponsors of this proposal were also addressed to the sponsors of #200725500. The sponsors of the latter proposal were able to provide responses sufficient to address ISRP comments.

For full comments on "restore and protect" type projects, please see heading "General comments concerning Nez Perce Tribe proposals to protect and restore various watersheds" at the beginning of the ISRP comments on project # 199607702, Protect & Restore Lolo Creek Watershed.

The ISRP carefully reviewed the series of Restore and Protect proposals in the Clearwater Subbasin for justification based on a "needs" prioritization; assessment of expected impact to habitat at a coarse level and to focal species at a fine level, and an appropriate level of M&E.

The sponsors appear to have misinterpreted the ISRP's original review comment pertaining to justification for this project's elements (including barrier removal). The ISRP sought justification of each specific project based on the quality and quantity of habitat above a barrier and the potential increase in fish use and benefit. Here, the ISRP recommends as a precursor (perhaps as a future stand alone project) a quantitative evaluation of habitat quality and quantity above each barrier, and that these estimates should play a major role in prioritizing barrier replacement/removal projects.

An additional rationale for requesting a project prioritization was to guide Council as to which project(s) of the group similarly submitted might yield greatest and lasting biological response to focal species per investment. Ultimately, the sponsors provided a ranking regarding this and similar projects. While the process was not transparent, nonetheless, this particular project was listed toward the bottom half of ~20 or so similar projects.

For full comments on "restore and protect" type projects, please see heading "General comments concerning Nez Perce Tribe proposals to protect and restore various watersheds" at the beginning of the ISRP comments on project # 199607702, Protect & Restore Lolo Creek Watershed.