This research proposal has numerous elements that could significantly improve restoration techniques and management of fish habitat in the Columbia River estuary (CRE). The research uses novel techniques to address critical hypotheses. Because processes supporting estuarine food webs in the Columbia River estuary often reflect both oceanic and freshwater habitats, research in this area is complicated and the proponents have put forth excellent ideas about how to unravel some of the ecological relationships. Some of the models proposed are particularly valuable. The multidisciplinary team is very capable - this is an excellent group of experienced estuarine researchers. The project has collaborative linkages with several other Columbia River estuary projects such as the monitoring program sponsored by the US Army Corps of Engineers. The investigation of power peaking on elevations and habitat availability is very worthwhile and could tie into other projects upriver, e.g., chum spawning channel projects.

The project has made substantial progress toward understanding historical and current habitat change in the estuary, improving physical models to simulate habitat change, and developing promising new techniques for understanding food webs and feeding habits of salmon in the estuary. Past results are well communicated via peer reviewed articles and reports. Technology transfer to habitat managers has been adequate but communication with hydrosystem managers could be improved.

However, this complex proposal would be enhanced by further information and clarification to help reviewers understand the integration of the various proposed tasks as well as responses to specific questions:

1. A brief discussion of how this research relates to the problem of estimating survival of juvenile salmonids in the estuary and the increments in survival that could be accruing from restoration would be helpful. This discussion could be put in the context of the results on restoration by some of the researchers (Bottom et al 2005) in the Salmon River, Oregon estuary.

2. The proposal would be improved by a flow chart showing the relationships between the numerous objectives and tasks. As presented the proposal describes two separate themes - the CORIE and modeling and historic reconstructions of physical factors, and the biology of the present populations and how they relate to two different habitat types. How are these two themes related?

3. The work in the Grays River estuary is well conceived and is linked with freshwater sampling which greatly improves understanding estuarine fish ecology. However, the proposal would be clarified by an explanation of how results from the smaller Grays River estuary (GRE) would be scaled up to the larger Columbia River estuary. On the other hand if the purpose of studying two estuaries is strictly for comparative purposes then it would be helpful to provide comments on the value of that particular approach. Is there a precedent for using a tributary estuary as a reference for a main stem river estuary?

4. The proposal would be clarified by explanation of the ecological models, specifically

The proponents have developed a model that apparently enables "prediction" of optimum fish habitat based on temperature, salinity, and depth (Bottom et al 2005, USACE, 2001). According to the proposal, this model will be a key element in estimating where and how much habitat needs to be restored. However, the model has not been published in a peer-reviewed journal and there are no plans for verification. The proposal would be enhanced by an update of any (anonymous) peer review of this model as well as a discussion of how the model would be verified.

Reviewers would appreciate further explanation of how the FRAGSTATS model would be used for planning/prioritization of estuarine fish habitat restoration. It would be helpful if the proponents explained how the model would work with juvenile salmon. The fish exploit and move between food patches and habitats at various time and spatial scales. Are there sufficient data on movement to calibrate the model? Does this model relate to the bioenergetic modeling (Task 5d)?

5. The proposal would be improved by a specific explanation of how otoliths and isotopes will be used to assess timing and residence, and an expansion of discussion on how isotopes will be used to distinguish organic matter sources, food webs and diet. An elaboration of findings in Roenger et al. (in press) as well as any update concerning anonymous peer review of their results would be helpful. Will these methods account for the possibility of individual fish moving back and forth between habitat types, confounding results for stable isotopes, parasites, and microchemistry?

6. The proposal would be enhanced by an explanation of which particular focal species/ESU that the project will relate to. Can the proponents reconcile use of hatchery chum in the Grays River estuary residency study with data needs for wild fish? The proponents state that this study and their related proposal on the Columbia River plume (199801400) will provide "spatial continuity for understanding out-of-basin impacts of FCRPS management on salmon populations." This is true as far as the modeling by Dr. Baptista is concerned; however, the ocean study generally targets coho and spring Chinook while the estuarine study targets ocean type Chinook, so there is little actual linkage or tracking of species passing through the estuary and into the ocean. It would be helpful if the proponents would explain connections between ocean and estuary components further.

7. Suggestions for increased information transfer from the project to hydrosystem staff and fishery biologists up river in the Columbia River Basin would be useful. Can linkages be improved between this study and others underway or proposed further upriver (e.g., those on reservoir type Chinook (see ISAB 2006-1; Crims Island restoration evaluation)(200734600)?

Caution is advised to avoid mortalities of non-focal and by-catch species in the trap netting and beach seining.