1. Objectives

The long-term goal of this project is to produce credible scientific insights for understanding the role of alluvial aquifers and associated hyporheic exchange relative to conservation of Pacific Northwest salmonids. This improved understanding was to provide a foundation for development of improved restoration strategies including location and design of projects. Unfortunately, the three major objectives are broadly stated and lack specific description of their intent and the specific hypotheses on which they are based. While the objectives are clearly worded, they are not quantitative or time bound. They function as main goal statements. For instance, the first objective was to understand the distribution of Chinook and summer steelhead, but there was no identification of the specific hyporheic attributes related to the distribution of the fish. The overarching hypothesis is equally broad and vague, simply stating that hyporheic exchange is important in the distribution of anadromous salmonids. Sub-hypotheses are provided in the description of current work, but these also are broadly stated and lack sufficient detail.

2. Methods

The proponents appear to have organized a comprehensive program. Previous annual reports describe their specific research measurements and analyses. Not only are the scientific methods sound, an Adaptive Management strategy and active Public Outreach activities are also key project components.

3. Results

The project has provided a substantial body of research on hyporheic exchange and its relation to the ecology of anadromous salmonids and habitat restoration. The project summary report describes the completion of Phase Two of a three-part project. Explanations of the measurements and analyses were provided in previous annual reports. The summary provides only general annual end dates for project activities.

While the body of research is scientifically sound, several conclusions are questionable. The researchers conclude that hyporheic exchange is an important consideration for management of spawning habitats because redds are found upstream of nick points. The research did not actually measure hyporheic exchange associated with the location of redds. Protection and restoration of a hyporheic exchange is warranted, but caution should be used in interpreting these results.

The Meacham Creek Restoration Project resulted in increased warming through the restoration reach. The project leaders attributed this to removal of riparian shade to allow large equipment to realign the channel. While this hypothesis may be correct, caution should be used in interpreting the results. Other physical processes could be responsible for the observed warming. The final project summary simply states that lack of shade counterbalanced the cooling effect without providing a qualifying statement that this was a hypothetical conclusion.

The hydrological model of hyporheic exchange, which was developed, is a beneficial tool in managing stream temperature. The inclusion of components addressing both shade and hyporheic exchange strengthens the model, and both are used by other researchers in modeling hyporheic processes.

The project has significant benefits for guidance for water temperature management and habitat restoration throughout the region. The proponents have made some interesting discoveries that have general benefits for restoration if a hyporheic perspective could be more broadly applied. The summary describes the benefit to habitat monitoring programs but also identifies a link between their hyporheic research and the First Foods management approach of the CTUIR River Vision. This linkage between habitat restoration in the First Foods concept is extremely important and should be highlighted in monitoring and presentations of their findings in the future. The summary would be strengthened by identifying additional outreach activities, which are provided in previous annual reports.

4. 2017 Research Plan uncertainties validation

The project addresses Critical Uncertainties (CUs) associated with the efficacy of stream and habitat restoration efforts [A 1.1, 1.2, 1.4, 2.2], while providing additional knowledge relevant to focal species response to restoration actions [E 1.1], and stream temperature response to climate change [J 1.3, 2.1].

The project summary briefly explained linkages between the research and the CUs but did not address whether the linkage was direct or indirect. In general, the ISRP agrees with the general description of linkages. One CU listed in the Council’s 2017 Research Plan Database (B. Mainstem habitat) was not included in the project summary. We agree that it is not closely linked to this research.

 

The project has provided important findings and potential general applications for a hyporheic perspective in restoration planning. After a number of years, however, results are less detailed than originally projected and, to date, are limited to the specific location studied. More information on biological responses and restoration applications would be useful. The proponents are asked to provide: • A quantitative description of the influence of hyporheic exchange on redd locations and the causes for warming in the restored reach of Meacham Creek; • A description of how past outreach and guidance has been incorporated into better management practices; and • Specific hypotheses, quantitative objectives, timelines, expected products, and the application of products for improved management practices associated with Phase 3 of the project. Note: The proponents provided an excellent response to a previous set of qualifications (i.e., 2007-252-00, Response to ISRP Memo dated 11/6/2013). They provided an outstanding example of direct, informative answers to questions raised in a previous ISRP request for response.

Comment:

The project continues to make impressive progress toward meeting its primary goals. The proponents have responded to the majority of past ISRP recommendations with new and revised project components and approaches. The project provides valuable information, analytical models, landscape applications, and restoration approaches for conservation efforts both within and outside the Columbia River Basin.

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

The project proponents responded constructively to the 2018 ISRP Research Review and, as well, developed explicit hypotheses, quantifiable objectives, and explicit timelines. This strengthens the research and provides a useful example for other projects. Timing of research components and objectives are clearly identified in the project timeline.

Important components for the project's technical foundations include (1) past project results that show that heat exchange between the channel and alluvial aquifer can influence main channel temperature regimes, (2) results supporting the conclusion that "stream restorations in alluvial valleys that consider the hyporheic zone have shown significant increases in juvenile salmonid use, including Meacham Creek, Rock Creek and Catherine Creek restoration efforts" and (3) that future modeling and land classification will provide tools to restore lost hyporheic potential across the Columbia Basin.

The technical foundation of the proponents' research is well documented and supported by their peer-reviewed publications.

The proposal not only describes benefits to habitat restoration programs but also identifies a link between their hyporheic research and the First Foods management approach of the CTUIR River Vision. This link between habitat restoration and the First Foods concept is extremely important and should be highlighted in the future.

2. Results and Adaptive Management

While there has been progress in quantifying the important components of the technical foundations of the project (summarized above), the ISRP notes limited confirmation-to-date through research and monitoring. The project attempts to confirm these relationships in the proposed activities. The five central activities for this project are logical extensions of ongoing activities (i.e., assessing salmon spawning locations with respect to thermal regimes indicative of hyporheic upwelling; the importance of floodplain shade in influencing hyporheic water temperatures; verifying and improving the TempTool model against empirical observations of hyporheic and channel water temperature; exploring the use of continuously logged temperature data; developing remote sensing classification and mapping methods to identify areas with high potential for hyporheic influence on stream temperature). Collectively, these activities address thermal issues that remain major challenges for conservation efforts in the Columbia Basin and provide tools that are potentially beneficial throughout the region and world.

The proponents describe a complex series of processes to provide adaptive management (AM). They have a regularly scheduled sequence of meetings both within the program and outside the research program with other decision-making processes of the CTUIR. Though it is not a strictly defined series of adaptive management steps, the identification of regularly scheduled coordination efforts and planned decisions provide the guidance and anticipated opportunities to adjust plans, consistent with a more formal adaptive management process.

3. Methods: Project Relationships, Work Types, and Deliverables

The ISRP greatly appreciates use of the SMART framework for the deliverables. This project was one of few proposals in this review to do so, and it illustrates a high level of expertise and strategic thinking for this project.

The ISRP found the proposal provided a clear outline of project activities. The detailed technical background and justification, as well as a clear set of proposed activities for the next phase, gave the ISRP confidence that the project has strong leadership and vision. The Gantt chart was also helpful in understanding the project's sequencing of the five activities.

The proponents are commended for their significant partnering with numerous and diverse groups, including other Tribes, USGS, USEPA, university researchers, and so forth, which expands the scope, impact, and dissemination of knowledge generated from this work.

The research methods and models are documented in peer-reviewed publications, past annual reports, and technical documents. The methods are well-suited for the research questions and field applications. The linkages between research components and on-the-ground restoration actions, both past and future, are a major strength of this project.

Qualification: This is an interesting project that has the potential to provide a useful approach and important information beneficial to habitat restoration. More detail could have been provided on how the project will link hyporheic processes and the geomorphic classification to restoration planning and actions, habitat effectiveness evaluation, and salmonid performances, as outlined in the comments below. The ISRP requests that the proponents produce a progress report that provides results to date and outlines a plan or study design that explicitly address these issues identified above. The progress report should be submitted within one year. The ISRP looks forward to reviewing this report.

The response provided a useful description of the method for determining reach scale hyporheic exchange based on LiDAR, geomorphic channel segment classification and Forward Looking Infrared (FLIR). According to the proposal the Hyporheic Potential Index (HPI) assessment for the Umatilla River has been concluded, but the estimation of this index needs to be completed for portions of the Grande Ronde and Walla Walla River subbasins. It was not clear whether HPI determination for the Umatilla would be repeated. Completion of HPI for the additional sites covered in the proposal is a worthwhile goal.

While the proposal describes the importance of floodplain reconnection to maintaining cooler water in channels where summer temperatures exceed the thermal tolerance of salmonids (e.g., breaching levees, restoring access to side channels, and removing other constraints to channel complexity to achieve "restoration of normative floodplain morphology") in general terms, it does not present direct evidence that existing restoration actions have facilitated surface-hyporheic water exchange to the extent that there have been reductions in summer stream temperature. For tributaries such as Meacham and Iskuulpa Creeks, in which there have been extensive restoration efforts, demonstrating that restoration of floodplain connectivity promotes hyporheic processes at the site scale is important. This should be a key objective of the project.

The project's goals have been clarified: "1) basin-wide assessments of potential hyporheic exchange (Hyporheic Potential Index; HPI) and stream temperature response in the target watersheds (Walla Walla, Umatilla and Grand Ronde) and 2) reach scale assessments of geomorphic characteristics associated with stream sections where hyporheic response drives variable temperature patterns (a subset of analysis in part 1)." The proposal mentions that temperature measurements of surface and hyporheic water will be monitored in [shallow] wells, but the locations of the well networks are not specified in the response, nor are funds for equipment such as temperature loggers and well building materials requested in the budget. The ISRP is still not certain about the extent and design of the field elements of this project, or other monitoring details. In addition, it was not clear how often FLIR flights would occur, and over what locations. FLIR technology is expensive, but more than one flight may be needed to locate parts of the stream network that experience unusually warm or cool waters. Additional details about temperature characterization, particularly in relation to ongoing restoration projects that affect hyporheic flows, would have been helpful.

The proposal emphasizes restoring natural channel morphological patterns as a key to maintaining habitable rivers in late summer, but we also wonder if shallow wells for irrigation water (if they occur) also might be having a significant impact on exchanges between surface and hyporheic flows.

The value of this project is not only in understanding hyporheic processes but also in using this understanding in evaluation of the effectiveness of habitat enhancement actions and in understanding salmonid use of hyporheic influenced areas. The proponents are well aware of these issues. They define two objectives but a third is evident. In several places in the initial proposal and in their response, they mention determining relationships between hyporheic influenced habitats and salmonid performances. However, in spite of their importance, little detailed information is given about how these studies will be conducted. Salmonid performances should be confined not just to redds and growth (if it has been measured) but should also include adult distribution and juvenile abundance and distribution, as these performances will respond to decreases in water temperature from enhanced hyporheic exchange.

An IMW project is planned for the Umatilla River. It would seem that the proponent's project would be beneficial to the IMW project and should be integrated with it. The proponents did not explicitly discuss their role, if any, in the IMW project.

The proponents should consider evaluation of hyporheic influences on reach scale thermal refugia along stream margins and in side channels. As the proponents are aware, these refugia can provide important habitats for salmonids even if hyporheic processes have little influence on mainstem temperatures.

This project can provide valuable information for stream habitat restoration programs throughout the Columbia River Basin. The presentation to the ISRP was good and alleviated many of our concerns about the soundness of the science behind the proposed work. The proponent’s presentation and response to questions demonstrated a solid grasp of hyporheic and riparian function. However, as the proposal now stands, the information provided was insufficient for scientific review. A response patterned after the presentation would be a good approach in responding to the ISRP’s concerns. The proponents need to provide more detail concerning study design, work elements, methods, and metrics for this proposal to be sufficient for scientific review. Specifically, the proposal needs to state whether the principal focus is on landscape-scale hyporheic identification using remote sensing tools or a more localized objective of assessing the effect of in-stream restoration activities on hyporheic-surface water interactions. We recommend that the project concentrate on one or the other, with additional details provided on where and how the studies would be carried out and the data would be analyzed and reported. We suggest that better integration with other regional habitat programs is needed. A more fully-developed adaptive management process should be provided. The proponents should explain how altered hyporheic flow was identified as an important limiting factor in the drainages to be studied? They also should discuss how the results of this project would be incorporated into watershed and reach scale restoration strategies. 1. Purpose, Significance to Regional Programs, Technical Background, and Objectives A better understanding of hypothetic processes in the Columbia River Basin could make a significant contribution to habitat and salmon restoration efforts. Although many habitat restoration projects have included increased hyporheic exchange as an objective, virtually none of the monitoring efforts associated with these projects have evaluated this process. This proposal contains the elements that would be required to conduct an evaluation of hyporheic exchange and how it is influenced by the application of stream channel reconstruction or other habitat enhancement measures. The development of a floodplain classification system that characterizes the nature and magnitude of hyporheic exchange based on field and remotely-sensed data sets also would be a valuable tool. But the proposal lacked sufficient detail to enable a through technical review. The technical background was well documented, although text was missing from some paragraphs in the Problem Statement. Even so, it was apparent that the proponents were familiar with the subject. One aspect of the technical background information that would have been helpful would have been a more complete discussion of the importance of hyporheic flows to salmonid production, and why the issue is so important in this region of the Columbia River Basin (e.g., water withdrawals have disrupted hyporheic-surface water exchanges). The proponents should explain how altered hyporheic flow identified as an important limiting factor in the drainages to be studied? Was the conclusion based on the lack of thermal refugia in the stream channels and evidence that restoring hyporheic flowpaths would create some cool water locations during the summer low flow period? The significance of the project to regional programs was inadequately described. The proposal describes how the project is integrated into the CTUIR restoration strategy. To what other restoration projects in these drainage systems is it related? The objectives were clearly stated and reasonably well supported. The objectives contained the only descriptions of the work elements in the proposal. 2. History: Accomplishments, Results, and Adaptive Management This proposal builds from a project on hyporheic processes that was completed last year in a reach of the Umatilla River. An annual report from this project was linked to the proposal, clearly indicating that the proponents of this proposal have the necessary experience and expertise to conduct the work. There was only a very brief paragraph in the proposal dedicated to adaptive management and this text simply stated that previous work in the Umatilla River had persuaded CTUIR habitat project leaders that hyporheic processes are important. More consideration should be given to the process by which the information and tools generated by this project will be delivered to project leaders and managers and the process by which this information could be used in the future restoration planning. The multi-scale aspects of this work, especially the development of a tool that will enable the identification of floodplain locations with high potential for hyporheic exchange, suggest that this project could have a direct effect on management decisions. As stated in the proposal, the project has been active for less than a year so there are few accomplishments to date. However, results of floodplain hyporheic flow mapping that are apparently in press were displayed. These results suggest that locations in the mainstem Umatilla River where hyporheic-surface water exchanges are significant are patchily distributed, as would be expected. Knowing where these places are is helpful in designing habitat restoration projects. There was little explicit discussion of how the results of this project would be incorporated into either overall watershed restoration strategies or into different types of restoration actions. 3. Project Relationships, Emerging Limiting Factors, and Tailored Questions for Type of Work (Hatchery, RME, Tagging) More information is needed on project relationships, particularly details on how this project would be integrated with other habitat restoration efforts – both CTUIR and other programs. A list of projects was provided with which this effort will “directly coordinate.” But the nature of the interaction was not described. Presumably, some of these projects will provide habitat treatments for before-after assessments of hyporheic processes. If so, these projects should be identified and a brief description of the types of habitat projects provided. One project was listed that did not seem to have any relationship with the proposed effort. Since this project will occur in the Walla Walla, Grande Ronde and Umatilla watersheds, why is the North Fork John Day River Basin Anadromous Fish Habitat Enhancement indicated as an effort with which this project will directly coordinate? Climate change or other emerging factors are not explicitly addressed in this proposal. 4. Deliverables, Work Elements, Metrics, and Methods Only a single deliverable is provided in the proposal: “Assess spatial and temporal relationships of hyporheic exchange, changing channel forms, geomorphic setting and altered temperature patterns.” As a generic deliverable, this is fine. But the introductory material in the proposal described a project that included a field effort at the project and reach scale coupled with a remote-sensing component to expand the finer-scale results. Deliverables articulated by spatial scale might have provided a clearer indication of project organization as the work elements associated with each scale are quite different. Although only a single deliverable was given, the executive summary gives two major objectives: (1) “the Multi-Scale Hyporheic Exchange project seeks to conduct a suite of field tests to document the changes in physical habitats related to surface/groundwater exchange. We anticipate that these activities will include field components for data collection and analysis, including, topographic data collection, dye releases and monitoring, temperature monitoring and tracer tests, as well as, analysis of field and remotely sensed data” and (2) “The second portion of this work seeks to develop a remote sensing-based classification of floodplains in the target watersheds (Umatilla, Walla Walla and Grand Ronde).” These two objectives should generate multiple deliverables. The work elements, metrics, and methods are only very briefly described in the proposal. These project elements appear to be generally appropriate for the objective and deliverable, but much more detail is required to enable a thorough evaluation of the experimental design and methodologies. Limited information was given on the field techniques and modeling methods, other than to list them without providing details about how they would be implemented at the proposed study sites. It is unclear how this project will be conducted, the locations of study sites, what measurement will be made and how they will be made. A major shortcoming of the proposal was that a study design was not provided. The lack of detail prevented a scientific assessment of the proposal’s merits. It appears that the evaluation of hyporheic functioning will take place at only one spatial scale (floodplain segments). What are the larger spatial scales and how will floodplain information be “rolled up” to these scales? What “distribution and characteristics of floodplain segments” will be assessed and how? How will floodplain characteristics be related to “salmon diversity and productivity?” The proponent states that they will evaluate how “geomorphically and thermally complex habitats affect growth and survival of juvenile salmon by using existing productivity datasets.” How will the relationship between habitat factors (presumably hyporheic influenced, but this is not clear) and fish growth and survival be determined? What data sets will be used?

Currently I am unaware of hyporheic parameters considered by the PNAMP rating criteria.

Floodplains are among the most productive areas of rivers for salmonid fishes. An important process influencing floodplain productivity is hyporheic flow that creates thermal regimes highly favorable for spawning, incubation, and rearing. The proposed work will identify hyporheic areas in subbasins, predict their effects on stream temperatures, and assess the importance of hyporheic flows fish productivity in floodplain habitats. The work addresses a critical need for habitat restoration in large rivers and is the only work of its kind in the Columbia River Basin. The work will help identify areas of subbasins where restoration would likely yield large benefits for salmonids.

The sponsors list an expected benefit as "classification all major floodplains in the Columbia River Basin." While this benefit may accrue in the future, the funded work should be restricted to the eight key test basins.

Technical and scientific background: Parts of the technical background are quite good. The graphics describing large-scale hyporheic analyses are excellent and would be a valuable addition to any subbasin analysis and plan. The background also makes a strong connection between hyporheic flow paths and stream cooling, which will certainly influence where some of the most productive segments of the drainage system for salmonids will be located.

There are also some questions that deserved greater attention. The actual influence of hyporheic flow (apart from temperature moderation) could have been more fully explored. Hyporheic zones influence nutrient dynamics, which in turn will affect stream productivity; however, nutrients are not really addressed. The ways in which anthropogenic disturbances have altered hyporheic development (and how these disturbances can be undone) also need to be addressed -- otherwise, how will the information generated by this project be effectively used? Are there some changes (e.g., severe downcutting) that have altered the hyporheos to the point that natural conditions can't be restored for decades or more? Can such changes be detected by the proposed analytical methods?

Although a minor point, some of the figures appeared to have been misplaced in the text (several pages from where they were referenced) and legends were missing, e.g., Fig. 2.

Rationale and significance to subbasin plans and regional programs: Developing a cost-effective, accessible technique for identifying areas with high hyporheic potential would clearly benefit subbasin plans. The selection of study areas would seem to be most applicable to Mid-Columbia and Columbia Cascade provinces. The stated goal of classifying "all major floodplains in the Columbia River Basin" would seem to be a bit optimistic without a broader spectrum of study areas; e.g., none of the sites were located in tributaries of the Lower Columbia or Willamette River. However, for the area in which the study takes place, the project would likely provide valuable information.

Relationships to other projects: The proposal references many linkages but is not entirely clear about how these linkages would occur. For example, the statement "Outcomes of this project will be directly coordinated with several projects in the Umatilla River Basin; specifically, Quantitative Assessment of Migrating Upstream Lamprey, Project #9402600, Umatilla Habitat Project, #8710002, Walla Walla Basin Habitat Enhancement, #9604601, North Fork John Day River Basin Anadromous Fish Habitat Enhancement, #200003100, Walla Walla Basin Natural Production Monitoring and Evaluation Project, #200003900 and Characterize Genetic Differences and Distribution of Freshwater Mussels, #200203700" simply states the relationship but does not describe how the integration would be achieved; i.e., what products or information will be exchanged.

Nearly all the other projects are located in the Mid-Columbia and there is no mention of linkages to related projects in other parts of the basin. This would not be a problem except one of the project's objectives is to classify hyporheic potential throughout the Columbia River Basin, and referencing floodplain work in other areas would be helpful.

Objectives: The four objectives were clearly defined, although without much specificity with regard to products or timelines. The objectives also were not explicitly tied to elements of the Fish and Wildlife Program or to individual subbasin plans. The first three objectives describe the methods to be used for classifying floodplains with regard to hyporheic potential. These objectives were very specific.

The fourth objective (Relating the importance of hyporheic flows to fish use) was concerned primarily with relating areas with well-developed hyporheic flowpaths to spawner abundance. While this is worthwhile, many of the focal species may not be primarily floodplain spawners but instead may spawn in smaller montane streams. Juvenile salmonid abundance would certainly be worth associating with floodplains with well-developed hyporheic systems. Perhaps this component could be added to the project.

Objective 4 also states that geomorphically and thermally diverse stream segments will be related to salmon abundance, species diversity, and life history diversity. While this is also a worthy goal, the proposal does not provide a clear indication of how spatially defined existing biological data are, relative to the stream segments in question.

Tasks (work elements) and methods: For the geographic analyses, the proposal describes the methods very completely. For the biological parameters, not enough information is presented to adequately judge the methods. The investigators are experienced with the methodologies required for this work and have successfully applied the approach in the Umatilla basin.

Monitoring and evaluation: There are not very many places in the proposal where ground-truthing model predictions are mentioned. While this is probably not a problem in the Umatilla subbasin where CTUIR maintains a very complete database, it could be a real problem for areas of the Columbia River Basin that do not include study sites.

Facilities, equipment, and personnel: Facilities are well equipped for this work and the sponsors are well qualified with demonstrated peer-reviewed publication records.

Information transfer: The proposal mentions only online data storage and retrieval. There is no mention of reports, publications, or scientific presentations. The sponsors have a good record of peer-reviewed publications and surely results of this work will be published in scientific journals.

Benefits to focal and non-focal species: This project has the potential to be of great benefit to focal species if areas with high hyporheic potential can be accurately identified and either protected or restored. The effects of anthropogenic alterations such as diking, shallow water wells, stream downcutting, and removal of riparian vegetation are inadequately discussed. Protecting and/or restoring hyporheic potential should benefit non-focal species too.