The following qualifications are offered as advice to improve project design and monitoring, and should be addressed during contracting and subsequent proposals. No immediate response to the ISRP is required.

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

This proposal for the Red River along with ones for Newsome Creek, and Crooked and American Rivers is designed to restore habitat in the upper tributaries of the South Fork Clearwater River. The proposal includes a good summary of information relevant to the problems and limiting factors being addressed. 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 ISRP appreciates seeing consideration of Pacific lamprey and other trout species.

Two evaluations, the South Fork Clearwater Landscape Assessment and the Nez Perce Forest Plan, state that the South Fork and its upper tributaries have high potential for spring Chinook and steelhead production mainly due to topography and lack of development. Factors limiting the production of these species in the Red River were recently updated by the FCRPS BiOp Expert Panel Process and were also presented in the Red River Ecosystem Analysis at the Watershed Scale (EAWS). The limiting factors for Red River were identified as impaired channel complexity, elevated stream temperatures, passage barriers, and excessive sedimentation.

 Of the project’s nine objectives, eight address the limiting factors listed above, and four objectives, specifically reducing stream temperatures, reducing instream sedimentation, improving aquatic habitat diversity and complexity, and protecting and restoring riparian habitats list success criteria that can be measured. Desired end points for three others, removing anthropogenic barriers, restoring wetlands, and reducing the impact of existing roads, were not as fully developed. The end points for objective 1 (to increase anadromous fish productivity and production, and life stage specific survival through habitat improvement) still need to be defined. Targets for survival and productivity should be stated and the rationale used to establish them explained. Also, Objective 7 refers to Newsome Creek instead of Red River, which is presumably a typographic error.

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

Approximately two miles of channel was reconstructed at the “Red River Narrows.” To complete this project, two acres of mine tailings were removed and the floodplain was re-graded to increase the width of the floodplain from 30 feet to over 100 feet. Stream sinuosity was also increased from 1.0 to 1.3, and three meander bends were added. Forty-one instream structures consisting of LWD, log jams, cobble fans, rock vanes, and other arrangements were added.

To reduce sedimentation, 43 miles of unneeded roads were decommissioned and 13 miles of roads were improved. Working with the U.S. Forest Service, five fish passage barriers have been replaced or removed, and an inventory of road crossings over streams in the Red River subbasin has been completed. Riparian zones have also been replanted. For example, in the Red River Narrows project area approximately 27,000 herbaceous plants of the 1 to 5-gallon size were planted along with 1,654 confers. In another restoration site, the Red River Meadows, approximately 26,000 ten to twenty cubic inch herbaceous and woody stock were planted along with 5,461 woody plants.

Onsite evaluations and results from monitoring programs are being used to adjust restoration approaches. Project monitoring allowed adaptive changes to the size of trees, shrubs, and herbaceous plants placed in riparian zones, and to the techniques used to plant them. Larger plants are being used, and they are now planted in terraced rows and protected by sod embankments. Culvert replacement has also changed since the project began. Bottomless culverts or bridges are used instead of typical squash pipe culverts so that flood level flows may pass without a large increase in velocity. Additionally, the sponsors are also installing control structures above, below, and in replacement culverts to reduce head cutting. Road decommissioning techniques have also evolved with fertilizer application to disturbed areas being discontinued in favor of pre- and post-weed treatment to reduce the presence of noxious weeds. Finally, changes in project direction and scope have occurred to meet the provisions of the FCRPS 2008 BiOp.

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 the “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.

Evaluation of Results

This project first received funding in 2007, but the year of reconstruction of Red River Narrows was not mentioned. Significant changes in sinuosity and the presence of instream structure are evident in aerial photographs following reconstruction of two miles of channel in the Red River Narrows. However, it is not clear to what extent the reconstruction efforts have been successful according to the project's criteria. The limited temperature data were not helpful. Information on survival of plantings was more informative and indicates some success.

The extent to which Chinook and steelhead populations benefitted is also unclear and presumably unknown.

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

Collaboration with U.S. Forest Service staff stationed at the Nez Perce Clearwater National Forest is an important component of this project and the other three NPT restoration projects in the South Fork Clearwater River (Protect and Restore the Crooked River and American River Watersheds, Lower South Fork Clearwater River Watershed Restoration, and Newsome Creek Watershed Restoration) all of which share resources, personnel, and equipment with the Red River Watershed Restoration Project. Other projects that complement the Red River project are the Nez Perce Tribal Hatchery, IDFG’s Red River Satellite Fish Hatchery, NPT’s B-run Steelhead Supplementation Effectiveness Research, and NPT’s Clearwater River Subbasin Focus Watershed Program.

Two emerging limiting factors were identified: climate change and non-native species. The proposal includes some thoughtful consideration of how proposed actions could ameliorate predicted effects of climate change. Culvert and bridge crossings are designed to withstand 100-year floods. Removing passage barriers has been given a high priority to provide access to cool water refuges in higher portions of the watershed when needed. Riparian plantings and reconnections to the floodplain are expected to help dampen the effects of climate change and provide some cooling influence.

Invasive plants are currently not regarded as a significant problem in the Red River, but weed treatment is routine on project sites where ground disturbance has occurred. Interactions between native salmonids and brook trout were mentioned as another possible emerging limiting factor. Brook trout are euthanized whenever they are captured in the project area to reduce the likelihood of deleterious interactions.

4. Deliverables, Work Elements, Metrics, and Methods

The project has seven deliverables. Four of them are directed toward resolving limiting factors for salmon in the Red River subbasin. Three of these, riparian planting in Red River Meadows, stream and floodplain restoration, and road improvement and decommissioning are well defined. Deliverable 1 (Stream crossings replacements) needs further elaboration. An inventory of creek crossings was completed and several processes were used to identify 56 apparent barriers. How these barriers will be prioritized for replacement or removal is not presented.

The remaining three deliverables deal with project management, potential property acquisition, and action effectiveness monitoring.

The end points for objective one, "to increase anadromous fish productivity and production, and life stage specific survival through habitat improvement" need to be defined. Targets for survival and productivity should be stated and the rationale used to establish them explained. In short, a better justification is needed. That is, what is the overall plan?

Also note the ISRP's programmatic comments on the South Fork Clearwater projects and the Nez Perce Tribe's (NPT) plan for monitoring and evaluation. Those comments reflect concerns about: 1) how to achieve adequate status and trends monitoring given cessation of Idaho Supplementation Study in 2013, and uncertainty about initiation of CHaMP in this area, which would support inferences from ISEMP. 2) how to justify habitat restoration given that past obstruction by Lewiston and Harpster dams have reduced current abundances of Chinook and steelhead adults in the South Fork Clearwater River and its tributaries to levels that are likely too low, even with supplementation, for their reproduction and growth to be limited by the spawning and rearing habitat currently available in these watersheds. Justification for habitat restoration in these watersheds appears to rest on the conviction that adult abundances will increase to recolonize available habitat ("build it and they will come"). Such an increase seems plausible, but no compelling evidence was presented to indicate that it is likely.

The following qualifications are offered as advice to improve project design and monitoring, and should be addressed during contracting and subsequent proposals. No immediate response to the ISRP is required.

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

This proposal for the Red River along with ones for Newsome Creek, and Crooked and American Rivers is designed to restore habitat in the upper tributaries of the South Fork Clearwater River. The proposal includes a good summary of information relevant to the problems and limiting factors being addressed. 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 ISRP appreciates seeing consideration of Pacific lamprey and other trout species.

Two evaluations, the South Fork Clearwater Landscape Assessment and the Nez Perce Forest Plan, state that the South Fork and its upper tributaries have high potential for spring Chinook and steelhead production mainly due to topography and lack of development. Factors limiting the production of these species in the Red River were recently updated by the FCRPS BiOp Expert Panel Process and were also presented in the Red River Ecosystem Analysis at the Watershed Scale (EAWS). The limiting factors for Red River were identified as impaired channel complexity, elevated stream temperatures, passage barriers, and excessive sedimentation.

 Of the project’s nine objectives, eight address the limiting factors listed above, and four objectives, specifically reducing stream temperatures, reducing instream sedimentation, improving aquatic habitat diversity and complexity, and protecting and restoring riparian habitats list success criteria that can be measured. Desired end points for three others, removing anthropogenic barriers, restoring wetlands, and reducing the impact of existing roads, were not as fully developed. The end points for objective 1 (to increase anadromous fish productivity and production, and life stage specific survival through habitat improvement) still need to be defined. Targets for survival and productivity should be stated and the rationale used to establish them explained. Also, Objective 7 refers to Newsome Creek instead of Red River, which is presumably a typographic error.

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

Approximately two miles of channel was reconstructed at the “Red River Narrows.” To complete this project, two acres of mine tailings were removed and the floodplain was re-graded to increase the width of the floodplain from 30 feet to over 100 feet. Stream sinuosity was also increased from 1.0 to 1.3, and three meander bends were added. Forty-one instream structures consisting of LWD, log jams, cobble fans, rock vanes, and other arrangements were added.

To reduce sedimentation, 43 miles of unneeded roads were decommissioned and 13 miles of roads were improved. Working with the U.S. Forest Service, five fish passage barriers have been replaced or removed, and an inventory of road crossings over streams in the Red River subbasin has been completed. Riparian zones have also been replanted. For example, in the Red River Narrows project area approximately 27,000 herbaceous plants of the 1 to 5-gallon size were planted along with 1,654 confers. In another restoration site, the Red River Meadows, approximately 26,000 ten to twenty cubic inch herbaceous and woody stock were planted along with 5,461 woody plants.

Onsite evaluations and results from monitoring programs are being used to adjust restoration approaches. Project monitoring allowed adaptive changes to the size of trees, shrubs, and herbaceous plants placed in riparian zones, and to the techniques used to plant them. Larger plants are being used, and they are now planted in terraced rows and protected by sod embankments. Culvert replacement has also changed since the project began. Bottomless culverts or bridges are used instead of typical squash pipe culverts so that flood level flows may pass without a large increase in velocity. Additionally, the sponsors are also installing control structures above, below, and in replacement culverts to reduce head cutting. Road decommissioning techniques have also evolved with fertilizer application to disturbed areas being discontinued in favor of pre- and post-weed treatment to reduce the presence of noxious weeds. Finally, changes in project direction and scope have occurred to meet the provisions of the FCRPS 2008 BiOp.

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 the “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.

Evaluation of Results

This project first received funding in 2007, but the year of reconstruction of Red River Narrows was not mentioned. Significant changes in sinuosity and the presence of instream structure are evident in aerial photographs following reconstruction of two miles of channel in the Red River Narrows. However, it is not clear to what extent the reconstruction efforts have been successful according to the project's criteria. The limited temperature data were not helpful. Information on survival of plantings was more informative and indicates some success.

The extent to which Chinook and steelhead populations benefitted is also unclear and presumably unknown.

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

Collaboration with U.S. Forest Service staff stationed at the Nez Perce Clearwater National Forest is an important component of this project and the other three NPT restoration projects in the South Fork Clearwater River (Protect and Restore the Crooked River and American River Watersheds, Lower South Fork Clearwater River Watershed Restoration, and Newsome Creek Watershed Restoration) all of which share resources, personnel, and equipment with the Red River Watershed Restoration Project. Other projects that complement the Red River project are the Nez Perce Tribal Hatchery, IDFG’s Red River Satellite Fish Hatchery, NPT’s B-run Steelhead Supplementation Effectiveness Research, and NPT’s Clearwater River Subbasin Focus Watershed Program.

Two emerging limiting factors were identified: climate change and non-native species. The proposal includes some thoughtful consideration of how proposed actions could ameliorate predicted effects of climate change. Culvert and bridge crossings are designed to withstand 100-year floods. Removing passage barriers has been given a high priority to provide access to cool water refuges in higher portions of the watershed when needed. Riparian plantings and reconnections to the floodplain are expected to help dampen the effects of climate change and provide some cooling influence.

Invasive plants are currently not regarded as a significant problem in the Red River, but weed treatment is routine on project sites where ground disturbance has occurred. Interactions between native salmonids and brook trout were mentioned as another possible emerging limiting factor. Brook trout are euthanized whenever they are captured in the project area to reduce the likelihood of deleterious interactions.

4. Deliverables, Work Elements, Metrics, and Methods

The project has seven deliverables. Four of them are directed toward resolving limiting factors for salmon in the Red River subbasin. Three of these, riparian planting in Red River Meadows, stream and floodplain restoration, and road improvement and decommissioning are well defined. Deliverable 1 (Stream crossings replacements) needs further elaboration. An inventory of creek crossings was completed and several processes were used to identify 56 apparent barriers. How these barriers will be prioritized for replacement or removal is not presented.

The remaining three deliverables deal with project management, potential property acquisition, and action effectiveness monitoring.

Modified by Dal Marsters on 6/11/2013 3:34:16 PM.

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.

It appears that there is a generally solid strategic basis for selection and development of this project. The use of subbasin and watershed scale assessments help to provide a foundation for restoration planning. However, given the high average gradient of the mainstem (7.3%), it seems likely that there are potential, natural and/or anthropogenic passage issues that have not been fully addressed. Planning documents indicate Leggett Creek is a high priority and an important stream for Chinook and steelhead. Additional information on how many miles of stream habitat will benefit from the proposed restoration, and some estimate describing the number of adults currently using the stream and/or juvenile densities would have been helpful. Based upon the current information, the proposed work appears to have some potential for fish benefits, but its priority would appear relatively low.

There was some question to understand why "excess fill from FS Road 469" was on the opposite side of the stream from the road. This material must be from dredge mining? Additional clarification would have been useful.

Without additional clarification, the ISRP continues to have questions about the value of the Leggett Creek restoration work, particularly the fish passage project at Highway 14. These questions are due especially to the high average gradient (7.3%) for the 5.6 miles of the mainstem that provide anadromous fish habitat. This steep a gradient would normally indicate less than optimum habitat for steelhead and spring Chinook salmon. The high average gradient also suggests a relatively high potential for upstream barriers both natural and anthropogenic. It is requested that the following additional information be provided at the time of contracting. 1. Length of anadromous fish habitat that will be accessed by the fish passage project. 2. Identification of any other natural or anthropogenic barriers that are blocking historical or potential anadromous habitat on the mainstem or major tributaries. 3. Additional discussion regarding the quality and productivity of the accessed habitat, particularly for steelhead and spring Chinook salmon. Also any details that may be available on current and historical salmon populations would be helpful. This information will be particularly helpful to better understand the sponsors statement "For both spring Chinook and steelhead, Leggett is considered a 'historic stronghold' for habitat and population status and rates a 'very high' in potential for habitat."

This is a solid proposal with a strong conceptual basis for restoration work. There is good use of a variety of planning documents including a broad scale landscape assessment. The project includes excellent delivery of projects and cost and skill sharing with partners. The proposal actually reflects many of the desired features of ecosystem restoration at the watershed scale. Their appears to have been substantial work to respond to ISRP comments on Technical and scientific methods and on project prioritization, although some questions remain on timing and prioritization of watersheds and related assessments that are planned.

Response requested: More detail is needed to justify why the reconstruction of 1/3 mile of new channel in a previously dredged site on Leggett Creek is expected to be worthwhile, how the reconstruction is to be done, and what alternatives to the reconstruction were considered and why were these alternatives not implemented.

Some additional items, that can be dealt with in contracting include:

1) How much habitat quality and quantity might be gained by this major restoration effort at the end of the proposal period (2018) and how does this compare with the habitat improvement goal of 14%, as required by the RPA? Do the sponsors think this effort will achieve the RPA goal? If not, how much more work is needed?

2) There are questions regarding the timely completion and content of the NPT Monitoring Plan that is under development.

3) Regarding road decommissioning and improvement, NOAA's goal is 1 mile of road per square mile or less. The sponsor has demonstrated that they have the tools to refine this target based on local information. In discussions, it was agreed that the NOAA number is highly unlikely to be reached and a more strategic approach will be needed with the key being to look at which road will give the best sediment reduction response. Additional discussion on this would be useful.

4) More discussion on what are the strategies to avoid weed control in perpetuity? The sponsors are looking at biocontrol methods, and a primary strategy is planting trees. They are also looking at prevention such as wash stations for equipment. Their weed spray contracts with the County have not had great success. It appears that there is a need for a cottage industry that targets spraying rather than doing broadcast spraying of entire hillsides. An advantage is that Weed Management Areas (WMAs) have been identified.

See the ISRP programmatic comments on the Clearwater River projects.

There were initial ISRP questions regarding whether there were active efforts to prevent further degradation of habitat associated with ongoing and future management activities. A good discussion of this was provided in the presentation portion of the review.

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

This is a long term project that has recently been expanded to provide for treatment of a larger land area in the South Fork Clearwater. The rationale for this expansion appears to be well-founded. The project is well-organized and generally strategic in its approach to restoring aquatic ecosystems. The strong partnership allows access and use of a broad range of multi disciplinary skills and is a major strength of the work to address issues at the watershed scale. There is a solid technical basis provided for the work and a good discussion of key processes and associated approaches for treating them. Use of a broad scale landscape assessment is an excellent tool for understanding conditions and processes and to provide a context for watershed and project scale planning. Good examples of this include the discussion about roads as a primary source of sediment and the focus of riparian treatments on tributary streams to more effectively address elevated stream temperatures.

The proposal also noted that IDEQ has done extensive work to establish Total Maximum Daily Loads (TMDLs) for temperature and sediment for the water quality limited streams and segments. It would be helpful to know if a Water Quality Restoration plan has been developed and if it has been integrated into the current proposal for restoration treatment.

The prioritization of limiting factors provides a good basis for understanding the context of the work. However, the limiting factor summary as weighted by the BiOp Expert Panel is the keystone of the limiting factors section. If, as shown, sediment is given a 38% value (twice that for temperature, barriers, or riparian condition) does that not mean sediment is the dominant problem and should receive priority in designing rehab actions? The proposal seems to give all putative limiting factors equal weight. Further discussion of the link between the focus of restoration work and the listed limiting factors and weights would be useful.

It is stated that the NPT have had numerous discussions on which watersheds are priority for treatment, yet no results of those discussions are provided. A summary would be helpful.

The proposal described its significance to salmon recovery and to programs in the region. Limiting factors were described and used in a process to identify and prioritize habitat restoration and protection activities. The goal for habitat quality improvement in the watershed as described in the BiOP RPAs (14%) was described. Quantitative objectives and deliverables for habitat restoration actions were described, thereby allowing reviewers to have an idea of how much improvement would be accomplished with the $4.37 million during the next five years. A monitoring program and linkages to associated monitoring efforts were described. Overall, the proposal was well written, and the significant effort was justified. However, it would be good to know how much habitat quality and quantity might be gained by this major effort at the end of 5 years, and how this compares with the goal of 14%, as required by the RPA. Do the sponsors think this effort will achieve the RPA goal? If not how much more work is needed?

This project’s stated goal is to restore the Lower South Fork Clearwater River (LSFC) aquatic ecosystems so that the habitat within these watersheds no longer limits recovery of the ESA Threatened South Fork Clearwater Steelhead population. There are some questions regarding Chinook and other fish species. Do they receive specific consideration during planning? From other portions of the proposal, it appears not. Additional review might indicate if anything is being missed that might be critical to bull trout or Chinook?

Additional maps would have been useful in better understanding the proposal and the locations of various past and proposed treatments.

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

A long list of accomplishments is provided, and a good track record of efforts to quantify the results is demonstrated, especially for sediment and temperature. Not presented in the main body of the proposal, although a hot link is provided, is some very informative effectiveness monitoring of physical parameters associated with fish passage restoration. This appears to be very thorough and to provide some excellent insights into the functioning of the treated sites. There was less information provided on the results of riparian planting. Of the 71 thousand trees and shrubs planted since 1996, what percent are alive now?

The material on stream temperatures over time is useful but needs additional evaluation to determine whether real declines in temperature have occurred. Figure 7 showing conditions Before/After treatment, but at different seasons, should be deleted. A more powerful assessment would have been between treatment and control locations over time. The design and justification of the temperature objective needs some substantial strengthening. The use of some basic temperature modeling, like that used by the former Potlatch Corporation, needs to be incorporated. It is not clear if that has occurred as part of the IDEQ work.

Some indications of positive results are shown for Meadow and Mill creeks where work has been ongoing for ca. 18 and 13 years, respectively. The sediment criterion being used is 30%, versus a 20% target given in the objective. What is basis for the discrepancy? More importantly, what are sediment conditions throughout the project area where cobble embeddedness is measured? Is it a useful metric? What is the percentage of fines in locations where spawning is actually occurring? Perhaps a more focused objective regarding conditions for spawning habitat would provide a more realistic and useful target.

There is a good discussion of adaptive management as related to project level work. This helps to show how lessons learned have been incorporated into the current and proposed restoration activities. Programmatically, it is stated that a formal adaptive management process will be provided as one section of a watershed scale monitoring plan (NPT). This plan is currently under development and a review draft scheduled for June 2013 and a final by December 2013. It would be helpful to know the current status of the plan relative to this schedule. This issue is discussed more in the Programmatic Comments.

Evaluation of Results

There is useful information provided on results of work for fish passage, sediment delivery/deposition, and elevated stream temperatures. Unfortunately, the watershed-wide context of the fish passage improvements is incomplete due to the need for additional assessments of a large number of road stream crossings in the treatment area. There is information provided to show some positive trends in stream temperature while results for fine sediment are not entirely clear at this point. Some improvements in this monitoring are discussed in item 2 above.

It is stated that PIBO has been monitoring habitat status and trend in the watershed for many years, yet no information is provided to show any potential results from this work. This information would help to better understand any changes in habitat quality and complexity over the period of active restoration.

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

There is a good discussion of climate change, non-native terrestrial plant effects, and the design of treatment strategies to respond. There is mention of non-native aquatic species, specifically brook trout, but little further discussion is provided on this topic other than they do not appear to currently represent a major problem. Further discussion of potential issues associated with non-native species would be helpful, particularly given the presence of bull trout in the area.

It would be useful to see some additional discussion of climate change and forest health, which appear to be potential major areas of concern given the possible risk of larger, more intense wild fires and related effects to riparian and aquatic habitat.

For the proposal area, it appears that nearly all of the land is on federal or Tribal properties. If some land is privately held, it would be good to know if private landowners will hinder or help the restoration efforts. Also, are there ongoing activities on Tribal and Forest Service lands such as logging and road building that might impact stream habitat quantity and quality? This and other proposals seem to ignore ongoing activities that might offset the improvements that are being made. This concern was discussed in more detail on the site visit portion of the review.

Also, hatchery supplementation efforts were briefly described. Additional discussion of this effort would be beneficial. How many fish are stocked? How many hatchery and wild fish return as adults? Is there evidence of density dependent growth, migration, or survival? How long will hatchery supplementation continue and to what extent does it contribute to harvests? What are the harvest goals for hatchery and wild salmonids in the watershed, and how are harvests managed now to conserve the wild stock?

4. Deliverables, Work Elements, Metrics, and Methods

There is a detailed list of deliverables and their linkage to key processes and associated limiting factors. The metrics for the deliverables appear to be appropriate except for riparian planting where numbers of plants is provided yet the objective relates to 75% expected plant communities. There is no linkage between the two items provided. There is good use of GRAIP to identify and prioritize road segments for improvement. It would be useful to know if this information is also used to identify roads/segments selected for decommissioning. There remain some questions on the background and justification for Deliverable 5, Leggett Creek. This is discussed in initial comments regarding the response requested by the ISRP. Additional maps would have been useful in better understanding location and details of work described.

Specific comments on protocols and methods described in MonitoringMethods.org

Current implementation and effectiveness monitoring has demonstrated some results. There is acknowledgement of the need for improvement and response through development of a watershed monitoring plan. Transition to ISEMP/CHAMP and AEM is discussed and is to be incorporated into this plan. This approach appears to be sound. It would be useful to know if this effort is on track for a June 2013 draft, and for the draft to be reviewed. This suggestion is discussed in the Programmatic Comments.

It is less clear how non-BPA funded monitoring will be integrated into the program in the future. Of particular note, given CHaMP, is the lack of consideration of future plans for PIBO despite its long history of monitoring in the watershed. This appears to be a major opportunity to examine the potential benefits of coordination and partnerships between the two programs.

Modified by Dal Marsters on 9/27/2013 11:07:02 AM.

The funding qualifications are (1) that actions to stabilize stream banks are fundable only if the bank reinforcements are done by planting vegetation, installing simulations of naturally lodged wood debris, or bioengineering methods that will eventually allow natural rates of channel migration, i.e., funding for hard-engineered structures, such as ones built primarily of rock is not justified, and (2) preparation of an appropriate, clearly organized and well-designed monitoring and evaluation plan must be done for this project.

The project's purpose is to protect and restore Red River habitat for fish. The sponsors take a watershed approach. It includes work to treat upland, riparian, and instream problems. In particular, actions will protect existing productive riparian habitats from human disturbance and development. Protection and restoration are needed with respect to damage caused by such human activities as urbanization, livestock grazing, mining, road building, logging, channelization, agricultural activities, and even recreation. Much of the proposed actions involve road improvement and decommissioning to reduce stream sedimentation and culvert replacement to remove fish migration barriers. The focal species are Chinook salmon, steelhead, and Pacific lamprey. The secondary species include four other salmonids and mountain whitefish. Other animals expected to benefit include moose, elk, and deer.

Upon receiving ISRP review comments, the sponsors discovered they had mistakenly included the 2002 Provincial Review Narrative in their proposal submission instead of the 2007 version. This complication resulted in various ISRP comments that are no longer applicable. We have tried to disentangle them from the extensive re-review that was needed.

The ISRP called for Ecosystem Analysis at the Watershed Scale (EAWS). The response clarifies that this analysis was done in 2002, and how the project plan relates to it. The project's emphasis is on roads and road rehabilitation, but the value of improved aquatic habitat is clearly recognized in the proposal.

The sponsors also noted that this proposal is tied to other important initiatives within the subbasin and the Columbia Basin. Significance to the subbasin plan is adequately shown, as are relationships to other projects.

The ISRP commented that, because funding actually began in 2002, a response was needed which includes a more thorough and quantitative summary of results produced to date. The correct narrative and the response document provide a more quantitative summary of the project's accomplishments to date. These are mainly statements of actions performed, and, of course, many physical and most biological results may not be detectable until more years have passed.

The long list of work elements and methods in Section F was not organized in hierarchical fashion to show how the elements related. Organization of work elements by objective exists in that section's table. The table is a useful supplement but does not substitute for narrative text, which would be more informative. This proposal, like several others did not bother to incorporate much narrative into Section F (objectives, work elements and methods). This made it hard to know in many respects what is actually planned for the methods.

The ISRP is concerned that the project's plans for in-channel restructuring may focus too much on rock work (boulders). Emphasis on "softer" forms of soil bioengineering using live, flexible woody vegetation in combination with root wads and other wood "debris" is recommended. The proposal's statement, "working to stabilize stream banks and create pools," conveys good intent but is much too vague. Inappropriate techniques of bank stabilization would harm fish habitat. The use of such hard-engineered structures as rock riprap and rock "vanes" or "J-hooks" (not specified in this proposal but implied or at least not ruled out) would not be justifiable, given the evidence provided. Qualification is placed on the funding recommendation partly for this reason.

The ISRP suggests that choice of technique depends greatly upon the quality of the fluvial geomorphologic analysis, which should address whether the stream is stable, incising, or aggrading. Only when the dynamic state of the stream is known can structural work be confidently proposed with the understanding that it is unlikely to become scoured out or buried in sediment.

The project's M&E plan still needs to be organized as such and presented in detail. In the present ("correct" 2007) narrative, the probable M&E elements are still scattered among the unorganized list of work elements. This is a major deficiency, which accounts for another part of the recommended funding qualification.

The ISRP recommended that, in the response loop, the Nez Perce Tribe prioritize and rank the numerous proposals submitted under "protect and restore" titles. This was covered in response attachments. 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.