A CONCEPTUAL SPAWNING HABITAT MODEL TO AID IN ESA RECOVERY PLANS FOR SNAKE RIVER FALL CHINOOK SALMON
Statement of Work and Budget FY2006

BPA Project Number:  1994-069-00
BPA Project Title:  A CONCEPTUAL SPAWNING HABITAT MODEL TO AID IN ESA RECOVERY PLANS FOR SNAKE RIVER FALL CHINOOK SALMON
Contract Number: 00000652-0014
Contract Title:  Salmon Spawning
Performance/Budget Period: 10/01/2005-2/28/2007


CONTRACT DESCRIPTION SECTION

A Conceptual Spawning Habitat Model to Aid in ESA Recovery Plans
for Snake River Fall Chinook Salmon

Project Goal
The goal of this project is to develop a spawning habitat model that can be used to determine the physical habitat factors that are necessary to define the production potential for fall Chinook salmon (Oncorhynchus tshawytscha) that spawn in large mainstem rivers like the Hanford Reach and Snake River.

Linkage to Fish Programs
This project addressed RPA Action 155 under the NOAA Fisheries 2000 FCRPS BiOp and continues to contribute to the ESA commitments made by BPA and the FCRPS Action Agencies under NOAA Fisheries' revised 2004 BiOp.  The goal of this project is consistent with the near-term RM&E hydrosystem targets included in the FCRPS Action Agencies' 2005-2007 Final Implementation Plan (IP).  The project is specifically listed for continued implementation in Table 22 of the IP and would help reduce hydrosystem uncertainties and provide status monitoring for restoring Snake River fall Chinook salmon spawning habitat

Status of Project
This project has been on-going since FY 2002.  It was originally scheduled to be a three-year project, completed in FY 2004.  In FY 2004, it was obvious that the project would not be completed as planned.  This was (and continues) conveyed to BPA COTR, and also to the Council.  In fact, in May 2004 at the time FY 2005 budgets were being developed, the Project Manager sent a letter to Patty O'Toole that stated project funds would be required in FY 2005 and FY 2006 to complete the project as originally planned.  The reasons for this were (paraphrased from the letter):
• The aerial photography contractor hired in FY 2001 to take photographs of the salmon spawning areas did not deliver an adequate product.  As such, additional photographs were needed in FY 2002 that were not included in the original proposal.  This has slowed the progress on completion of other tasks.  
• The amount and complexity of data collected during the field work was greater than I anticipated.  As such, the completion of a database to manage these data has taken more time and resources than originally planned.  
• Additional data is needed to complete the spawning habitat model for the entire Hanford Reach.  Currently, the bathymetry data, which is a critical part of the model, is only available for the middle 15 miles of the Reach.  We anticipated there would be additional bathymetry data collected earlier in the study but it wasn't until the winter of 2003-2004 that the USFWS and the USGS, under a contract to the Columbia River Intertribal Fish Commission as funded by the State of Alaska, completed a SHOALS-LIDAR and bathymetric survey of the remaining 36 miles of the Reach.  We have been working with the contractors of that study to acquire this information from them.  We are hopeful this data will become available during FY 2005, and we will be able to include it in our spawning habitat model in FY 2006.  This additional data will provide us the ability to improve upon and refine our estimates of fall Chinook salmon production potential for the entire Reach, and will result in a better product that is transferable to other areas.
Although behind pace, the project continues to meet the scope and the goals of the original proposal submitted during the FY 2002 rolling review. The ISRP specifically noted that this project is a major study of the Hanford Reach and recommended "applying their methods in other spawning areas of the basin".  This is occurring.  The information from this project is being used in other parts of the Columbia River Basin, both as a source of technical information on the biology of ESA listed salmon (e.g., Ives Island, Grays River, Snake River) but also as a conduit of information-exchange in project implementation.  Continued investment in this major project is worthwhile given the importance of the Hanford Reach as a production area for fall Chinook salmon and the lessons we are currently learning and already applying to other parts of the basin including listed populations within the Snake River.
Background
Current mainstem production areas for salmonids are now largely restricted to habitats that remain non-inundated, i.e., the Hanford Reach of the Columbia River and the Hells Canyon Reach of the Snake River (Dauble and Watson 1997; Groves and Chandler 1999; Battelle and USGS 2000).  Although the Hanford Reach stock of fall Chinook salmon is relatively healthy (Huntington et al. 1996; Dauble and Watson 1997), the Snake River fall Chinook salmon were listed under the Endangered Species Act (ESA) in 1994.  The Hanford Reach may be considered as having the only "core population" of fall Chinook salmon within the Columbia River system (ISG 1996).  Recovery planning is underway for stocks listed under ESA and will rely on a combination of spawning habitat protection and restoration (NPPC 1994; NMFS 1995; Dept. of Commerce 1997), among other actions.  If habitat in other portions of the basin can be protected, then the core population of fall Chinook salmon in the Hanford Reach may be able to seed depressed stocks (ISG 1996).  With limited recovery funding, it is important to find the specific habitats that should be protected and enhanced (Rondorf and Miller 1993).  
In both the Hanford Reach and Hells Canyon Reach the distribution of fall Chinook salmon spawning is patchy, suggesting there are specific habitat requirements that draw spawning fish back to particular areas (Geist et al. 1997; Geist and Dauble 1998; Geist et al. 2000).  Traditional methods to characterize spawning habitat have not adequately described this patchy habitat use because these methods involve measurements of depth, substrate, and velocity at the spatial scale of a redd rather than at the scale of the habitat forming features (e.g., Burner 1951; Swan 1989; Groves and Chandler 1999).  
Recent reviews suggest that salmonid spawning habitat in river systems is linked to the geomorphic characteristics of river channels that occur at various spatial scales (Frissell et al. 1986; Stanford et al. 1996; Imhof et al. 1996; Geist and Dauble 1998; Dauble and Geist 2000).  Rivers are highly interactive with the surrounding landscape within the floodplains of most rivers (Stanford et al. 1996; ISG 1996), and these interactions create connections between the ground water and surface water within hyporheic habitats.  Through funding provided by the Fish and Wildlife Program since 1994, we have been investigating the relationship between hyporheic flow and fall Chinook salmon spawning in the Hanford Reach (Geist 1998; Geist et al. 1997; Geist et al. 2000; Geist 2000).  Our research suggests that in spawning areas with equal amounts of depth, substrate, and velocity (i.e., micro-habitat characteristics), fall Chinook salmon spawning is more prevalent in areas of hyporheic upwelling (Geist 2000).  The hydrologic exchange that occurs within the hyporheic zone may be an important geomorphic process occurring within large river systems that affects where fall Chinook salmon spawn (Geist and Dauble 1998; Geist 2000).      
We recognize, however, that the current success and ultimate future of the Hanford Reach population is more than the quality of the spawning habitat.  Hanford Reach populations have increased during the past 25 years because suitable spawning and rearing habitat remained intact, runs were supplemented by hatcheries, and because the mainstem core population remained viable (Dauble and Watson 1997).  In contrast, populations in other parts of the Columbia and Snake rivers have declined because spawning areas were inundated, former core populations were effectively "closed-off" from important upriver production areas, and/or habitat quantity or quality of remaining riverine areas is poor.  These changes provide strong evidence that production potential of remaining mainstem fall Chinook salmon is influenced by abiotic conditions and that these conditions limit successful completion of life history requirements.  Therefore, we propose that in order to successfully manage healthy core populations like Hanford Reach fall Chinook salmon, a clear understanding is needed of the attributes that form the structure and function of the habitat they depend upon.  In the case of Hanford Reach fall Chinook salmon, this entails understanding the attributes of a healthy alluvial river.  
It is well established that stream flow quantity and timing are critical components of water supply, water quality, and the ecological integrity of river systems (Poff et al. 1997).   Flow regimes, geology of surrounding landscapes, and longitudinal slope are important controlling variables in salmon habitats and operate at both the watershed and reach scale (Imhof et al. 1996).  In the Columbia River, flow regimes are highly regulated by the hydroelectric complex and seasonal discharge is influenced by water storage and water use practices (Ebel et al. 1989).  Flow regulation also affects connections among groundwater, floodplains, and surface water (Stanford et al. 1996), or convergence zones (i.e., hyporheic habitats) where biodiversity and bioproduction are frequently high (Stanford and Ward 1993).  Hydrologic variables such as discharge become a controlling factor at the reach and site scale in regulated rivers.   The relative magnitude and frequency of high flow events also acts to modify channel form, but only within constraints of existing geological features.  For example, major floods are less frequent because of upstream flood-control projects constructed since the 1940s.  This change is significant because rivers that flood frequently maintain different species and food webs from systems that are more ecologically benign (Stanford et al 1996).  
Knowledge of the current status of the Hanford Reach as a functional ecosystem is critical to future recovery planning that involves manipulation of mainstem habitats and anadromous fish populations.  This information need is consistent with Reeves et al. (1995) notion that recovery programs need to consider ecosystem processes that create and maintain habitats through time (in addition to identifying causal factors that result in loss of habitat).  It is also consistent with the recommendations of independent scientists that increased attention be placed on healthy populations like those found in the Hanford Reach (ISRP 1998).  
If the Hanford Reach functions as an alluvial stretch of river it should exhibit attributes typical of coarse-bedded alluvial rivers (i.e., spatially complex channel morphology, natural variability in flows and water quality, periodic channel bed scour and fill, functional floodplain, etc.).  These alluvial attributes result in greater environmental heterogeneity or habitat complexity in the river continuum (Stanford et al. 1996).  Based on annual escapements that have remained relatively stable over the past 10 years at about 80,000 adults (Dauble and Watson 1997), it appears that the geological template and hydrologic conditions in the Hanford Reach are compatible with life history requirements of fall Chinook salmon.  However, it is unknown whether hydropower development and flow management practices have altered the physical attributes of the river to the point where fall Chinook production is below system capacity.   In other words, it appears that Hanford Reach fall Chinook are currently healthy but because of our limited understanding of the relationships between these fish and their ecosystem, we don't know if the population will continue to be healthy in the future.  Given the overall importance of the Hanford Reach population, this is a relatively high risk.
Project Objectives for FY 2006

There are two specific objectives for FY 2006.  Objective 1 is to complete data analysis, interpretation, and reporting (in the form of manuscripts) for the data collected since the Council review.  This is a priority and will be completed in 2006 by finishing data analysis, finalizing data interpretation, writing, and submitting to peer-reviewed journals several manuscripts.  Objective 2 is to acquire bathymetry data and begin revising our existing spawning habitat model for the upper and lower sections of the Hanford Reach; this data currently resides with the Columbia River Intertribal Fish Commission, US Fish and Wildlife Service, and/or the US Geological Survey.  As described above, the development of the spawning habitat model for the entire Reach was approved in the original proposal but subject to availability of bathymetric data.  Through a separate contract, this information is now available and if it can be acquired from the previously mentioned agencies, will be used to construct a revised spawning habitat model.

Location of Project

This project is designed to be conducted in the Hanford Reach of the Columbia River with application to the mainstem Snake River.

References
Battelle's Pacific Northwest Division and US Geological Survey, Biological Resources Division.  2000.  Assessment of the impacts of development and operation of the Columbia River hydroelectric system on mainstem riverine processes and salmon habitats.  Final Report Prepared for the Bonneville Power Administration, Portland, Oregon.
Burner, C.J.  1951.  Characteristics of spawning nests of Columbia River salmon.  Fishery Bulletin 52:95-110.
Dauble, D.D., and  D.G. Watson.  1997.  Status of fall Chinook salmon populations in the mid-Columbia River, 1948-1992.  North American Journal of Fisheries Management 17:283-300.
Dauble, D.D., and D.R. Geist.  2000.  Comparison of mainstem spawning habitats for two populations of fall Chinook salmon in the Columbia River Basin.  Regulated Rivers: Research and Management 16: 345-361.
Department of Commerce.  1997.  Final Rule on Endangered Species Listing for Evolutionary Significant Units (ESUs) of West Coast steelhead.  August 18, 1997.  Department of Commerce, Washington, D.C.
Ebel, W.J., C.D. Becker, J.W. Mullan, and H.L. Raymond.  1989.  The Columbia River-toward a holistic understanding. P. 205-219.  In D.P. Dodge (ed) Proceedings of the International Large River Symposium.  Canadian Special Publication Fisheries and Aquatic Science 106.
Frissell, C.A., W.J. Liss, C.E. Warren, M.D. Hurley. 1986.  A hierarchical framework for stream habitat classification: viewing streams in a watershed context.  Environmental Management 10:1099-214.
Geist, D.R.  1998.  Redd site selection and spawning habitat use by fall Chinook salmon.  Ph.D. Dissertation, Oregon State University, Corvallis, Oregon.
Geist, D.R. 2000.  Hyporheic discharge of river water into fall Chinook salmon (Oncorhynchus tshawytscha) spawning areas in the Hanford Reach, Columbia River.  Canadian Journal of Fisheries and Aquatic Sciences 57: 1647-1656.
Geist, D.R., and Dauble, D.D.  1998.  Redd site selection and spawning habitat use by fall Chinook salmon: the importance of geomorphic features in large rivers.  Environ. Manage. 22:655-669.
Geist, D.R., D.D. Dauble, and R.H. Visser.  1997.  The development of a spawning habitat model to aid in recovery plans for Snake River fall Chinook salmon.  Fiscal Year 1995 and 1996 Progress Report to the Bonneville Power Administration , Portland, OR.
Geist, D.R., Jones J., Murray C.J., and Dauble D.D. 2000.  Suitability criteria analyzed at the spatial scale of redd clusters improved estimates of fall Chinook salmon (Oncorhynchus tshawytscha) spawning habitat use in the Hanford Reach, Columbia River.  Can. J. Fish. Aquat. Sci. 57: 1636-1646.
Groves, P.A., and J.A. Chandler.  1999.  Spawning habitat used by fall Chinook salmon in the Snake River.  North American Journal of Fisheries Management 19: 912-922.
Huntington, C., W. Nehlsen, and J. Bowers. 1996. A survey of healthy native stocks of anadromous salmonids in the Pacific Northwest and California.  Fisheries 21(3):6-14.
Imhof, J.G., J. Fitzgibbon, and W.K. Annable.  1996.  A hierarchical evaluation system for characterizing watershed ecosystems for fish habitat.  Canadian Journal of Fisheries and Aquatic Sciences 53(Suppl.1): 312-326.
Independent Scientific Group (ISG).  1996.  Return to the river, restoration of salmonid fishes in the Columbia River ecosystem.  Pre-publication copy dated September 10, 1996.  Northwest Power Planning Council, Portland, OR.
Independent Science Review Panel (ISRP).  1998.  Review of the Columbia River Basin Fish and Wildlife Program for fiscal year 1999 as directed by the 1996 ammendment to the NW Power Act.  Northwest Power Planning Council, Portland, Oregon.
NMFS (National Marine Fisheries Service) 1995. Proposed Recovery Plan for Snake River salmon.  U.S. Department of Commerce, NOAA.
Northwest Power Planning Council. 1994.  1994 Columbia River Basin Fish and Wildlife Program.  
Poff, N. L., J. D. Allan, M. B. Bain, J. R. Karr, K. L. Prestegaard, B. D. Richter, R. E. Sparks, and J. C. Stromberg. 1997. The natural flow regime: A paradigm for river conservation and restoration. BioScience 47:769-784.
Reeves GH, LE Benda, KM Burnett, PA Bisson, and JR Sedell. 1995.  A disturbance-based ecosystem approach to maintaining and restoring freshwater habitats of evolutionary significant units of anadromous salmonids in the Pacific Northwest. AFS Symp. 17.
Rondorf, D.W., and W.H. Miller (eds.).  1993. Identification of the spawning, rearing, and migratory requirements of fall Chinook salmon in the Columbia River basin.  U.S. Department of Energy, Bonneville Power Administration, Portland, OR.
Stanford, J.A. and J.V. Ward 1993.  An ecosystem perspective of alluvial rivers: connectivity and the hyporheic corridor.  Journal of the North American Benthological Society  12:48-60
Stanford, J.A., J.V. Ward, W.J. Liss, C.A. Frissell, R.N. Williams, J.A. Lichatowich, C.C. Coutant. 1996.  A general protocol for restoration of regulated rivers. Regulated Rivers: Research  & Management, 12:391-413.
Swan, G.A. 1989.  Chinook salmon spawning surveys in deep waters of a large, regulated river.  Regulated Rivers: Research  & Management 4:355-370.