1
Introduction

The Columbia River and its tributaries constitute one of North America’s great river systems (Figure 1-1). The Columbia River Basin extends over an area of 258,000 square miles (Leopold, 1994), covering portions of seven U.S. states and one Canadian province. The river stretches 1,214 miles from its source in the mountains of the Canadian province of British Columbia to the Pacific Ocean. One of the Columbia’s main tributaries is the Snake River, which drains most of the basin’s southeastern reaches and enters the Columbia near the Tri-Cities (Kennewick, Pasco, and Richland) region of central Washington. Other important tributary streams are the Clearwater, Deschutes, Kootenai, Pend Oreille, Salmon, and Willamette rivers.

COLUMBIA RIVER SALMON

The Columbia River is well known for its rich variety of salmon species and populations. Columbia River salmon once existed in great abundance and for thousands of years served as the foundation of the diets of the region’s Native American tribes. Lewis and Clark described the abundance of Columbia River salmon during their expedition to the region in 1805 to 1806:

Captain Clark … halted at two large mat-houses. Here, as at the three houses below, the inhabitants were occupied in splitting and drying salmon. The multitudes of this fish are almost inconceivable. The water is so clear that they can readily be seen at the depth of 15 or 20 feet; but at this season they float in such quantities down the stream, and are drifted ashore, that the Indians have only to collect, split, and dry them on the scaffolds. (Coues, 1893, p. 641)



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Managing the Columbia River: Instream Flows, Water Withdrawals, and Salmon Survival 1 Introduction The Columbia River and its tributaries constitute one of North America’s great river systems (Figure 1-1). The Columbia River Basin extends over an area of 258,000 square miles (Leopold, 1994), covering portions of seven U.S. states and one Canadian province. The river stretches 1,214 miles from its source in the mountains of the Canadian province of British Columbia to the Pacific Ocean. One of the Columbia’s main tributaries is the Snake River, which drains most of the basin’s southeastern reaches and enters the Columbia near the Tri-Cities (Kennewick, Pasco, and Richland) region of central Washington. Other important tributary streams are the Clearwater, Deschutes, Kootenai, Pend Oreille, Salmon, and Willamette rivers. COLUMBIA RIVER SALMON The Columbia River is well known for its rich variety of salmon species and populations. Columbia River salmon once existed in great abundance and for thousands of years served as the foundation of the diets of the region’s Native American tribes. Lewis and Clark described the abundance of Columbia River salmon during their expedition to the region in 1805 to 1806: Captain Clark … halted at two large mat-houses. Here, as at the three houses below, the inhabitants were occupied in splitting and drying salmon. The multitudes of this fish are almost inconceivable. The water is so clear that they can readily be seen at the depth of 15 or 20 feet; but at this season they float in such quantities down the stream, and are drifted ashore, that the Indians have only to collect, split, and dry them on the scaffolds. (Coues, 1893, p. 641)

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Managing the Columbia River: Instream Flows, Water Withdrawals, and Salmon Survival FIGURE 1-1 The Columbia River basin. SOURCE: Available online at http://www.bpa.gov/power/pg/fcrps_brochure_17x11.pdf, last accessed June 18, 2004.. The Pacific Northwest and its salmon populations and habitat have undergone many changes in the 200 years following Lewis and Clark’s transcontinental adventure. The region has experienced substantial human population growth, and attendant land use changes have altered vegetation and hydrological patterns. Hydropower dams on the Columbia mainstem and hundreds of storage, diversion, and smaller-scale hydropower dams on its tributaries have altered the volume, velocity, and seasonality of river flows. The cumulative effects of these and other changes have contributed to a long-term decline in the number of

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Managing the Columbia River: Instream Flows, Water Withdrawals, and Salmon Survival View of Bonneville Dam, with its spillway and two powerhouses. Photo courtesy of Jeffrey Jacobs. adult salmon returning to the river to spawn. Historic annual runs of salmon and steelhead, believed to have been at times as great as 16,000,000 fish (NPCC, 1986), declined to about 1,000,000 by the 1990s (http://www.nwppc.org/library/pocketguide/pocketguide.pdf, last accessed November 20, 2003), and increased in the late 1990s and early 2000s. Six species of anadromous salmonids inhabit the Columbia basin: (1) Chinook salmon (Oncorhynchus tshawytscha); (2) coho, or silver, salmon (O. kisutch); (3) chum salmon (O. keta); (4) sockeye or red salmon (O. nerka); (5) pink or humpback salmon (O. gorbuscha); and (6) steelhead (O. mykiss). Chinook, coho, sockeye, and steelhead that migrate through the middle and upper reaches (above Bonneville Dam) of the Columbia and Snake rivers are all listed as federally endangered species. Columbia River salmon and steelhead stocks that are “threatened” or “endangered” (Table 1-1) under the Endangered Species Act include:

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Managing the Columbia River: Instream Flows, Water Withdrawals, and Salmon Survival TABLE 1-1 Federally Threatened and Endangered Columbia River Salmonid Species Endangered Species Steelhead Upper Columbia River Steelhead Chinook Salmon Upper Columbia River Spring Run Chinook Sockeye Snake River Sockeye Threatened Species Steelhead Snake River Basin Steelhead Lower Columbia River Steelhead Middle Columbia River Steelhead Upper Willamette River Steelhead Chinook Salmon Snake River Spring/Summer Chinook Snake River Fall Chinook Upper Willamette Chinook Lower Columbia River Chinook Coho Salmon Lower Columbia River/Southwest Washington Coho (candidate for listing) Chum Salmon Columbia River Chum Salmon   SOURCE: Data from NOAA Fisheries, National Marine Fisheries Service. Available online at http://www.nmfs.noaa.gov/prot_res/species/ESA_species.html, last accessed February 6, 2004. Snake River fall Chinook salmon, threatened (Snake River upstream from Lyons Ferry Hatchery to Hells Canyon Dam, including lower reaches of the Clearwater, Imnaha, Grande Ronde, Salmon, and Tucannon rivers). Snake River spring/summer Chinook salmon, threatened (wild/natural spawners in several subbasins of the Snake and Salmon rivers, including tributaries of the lower Snake River, Grande Ronde and Imnaha rivers, South Fork Salmon River, Middle Fork Salmon River, and the Upper Salmon River). Mid-Columbia River steelhead, threatened (tributaries in the Columbia Plateau region, including Rock Creek, Fifteenmile Creek, and the White Salmon, Klickitat, Yakima Deschutes, John Day, Umatilla, and Walla Walla rivers). Snake River sockeye salmon, endangered (Redfish Lake

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Managing the Columbia River: Instream Flows, Water Withdrawals, and Salmon Survival in the upper Salmon River basin). Upper Columbia River spring Chinook salmon, endangered (tributaries upstream from Rock Island Dam, including the Wenatchee, Entiat, and Methow rivers). Upper Columbia River steelhead, endangered (tributaries upstream from Rock Island Dam, including minor tributaries to the Columbia River and the Wenatchee, Entiat, and Methow rivers). Other Native and Exotic Fish Species The Columbia River, like many western U.S. rivers, has far fewer native fish species than similar-sized rivers in the central and eastern United States. Before the construction of dams, the native fauna was dominated by salmonids (salmon and trout), cyprinids (minnows), and cottids (sculpins), most of which are still present but often in reduced numbers. In addition to the salmonids mentioned above, the basin also supports populations of bull trout (Salvelinus confluentus) and coastal cutthroat trout (O. clarki). Bull trout are federally listed as threatened and are found throughout the Columbia River basin. They typically reside in upper-tributary streams, reservoirs, and lakes and are found occasionally in the mainstem Columbia River. The salmonid complex also included whitefishes and ciscoes. The largest cyprinid in the Columbia River is the northern pikeminnow (formerly known as the northern squawfish). The white sturgeon is usually anadromous (spending part of its life in fresh water and part in saltwater), but landlocked populations also inhabit the Columbia River basin (Lee et al., 1980). By the late twentieth century, the white sturgeon population had declined to a point at which they were no longer considered commercially viable in the lower Columbia River (Craig and Hacker, 1940). White sturgeon are today found in small numbers in distinct landlocked populations. Several species of lamprey also exist in the Columbia River. Counts of lampreys reveal greatly diminished populations (CRITFC, 1996), and there have been efforts to classify the species as threatened or endangered. Exotic or nonnative fish species have been widely introduced into the western United States and the Columbia River basin is no exception. The striped bass and the American shad, na-

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Managing the Columbia River: Instream Flows, Water Withdrawals, and Salmon Survival tive to the eastern United States, are nonnative anadromous species that inhabit the Columbia River. Other nonnative freshwater fish in the Columbia River system are largemouth bass, smallmouth bass, sunfish, crappie, walleye, carp, catfish, bullhead, brown trout, brook trout, and lake trout. Many of these species have thrived in the altered conditions of the Columbia River system; however, some may have been more productive in an undammed river. Many of these species prey on salmon eggs and fry, and some—especially larger individuals—eat salmon juveniles as well (Zimmerman, 1999). Among nonnative species, walleye have particularly been implicated in connection with reduced salmon population productivity. Smallmouth bass and channel catfish also prey on salmon, and these predators are more abundant in the upper Columbia and Snake rivers than in the lower Columbia (ibid). Commercial Fishing The earliest commercial activity in the Columbia basin may have been fishing, as Native American tribes caught and traded salmon products. The introduction of commercial fishing, processing, and distribution practices to the region in the late nineteenth century resulted in a burst of economic activity and the generation of a great deal of wealth. The intensity of commercial fishing eventually led to declines in salmonid fish populations in the early- to mid-twentieth century. According to one estimate, total salmon harvest peaked at an average of approximately 34,000,000 pounds per year between 1880 and 1930, then declined to 24,000,000 pounds per year in the 1940s, dropped to 11,000,000 pounds per year in the 1950s, and was recorded at 1,200,000 pounds per year in the early 1980s (Huppert and Fluharty, 1995). Today, little commercial fishing is allowed or even possible given the small stock sizes in the basin (ibid.). Between 1981 and 1993, total average annual landed value for commercial fisheries in the basin was about $6.8 million (1993 dollars). Roughly half of the commercial value is generated in connection with fishing allowed under the American Indian Treaty, which is based on the 1974 ruling by a federal judge regarding the balance between tribal and nontribal fishing (Chapter 5 discusses the Boldt decision and other Native American water issues).

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Managing the Columbia River: Instream Flows, Water Withdrawals, and Salmon Survival From 2000 to 2003 large runs of Chinook increased the commercial value of harvested salmon. However, the listing of several salmon and steelhead stocks in the Columbia River as threatened or endangered during the 1980s and 1990s triggered provisions of the Endangered Species Act, which in turn has limited opportunities for increased salmon harvests from more abundant (nonlisted) stocks. Chinook and coho salmon dominate the commercial fishing catch (93 percent), with white sturgeon also being important. Employment in fisheries is today relatively small, and in 1995 the salmon component was negligible because of low stock abundance. Depending on the assumption of annual income levels, the number of jobs currently dependent on the basin fisheries is estimated to be between 200 and 400 (Huppert and Fluharty, 1995). Although this is a small percentage of regional employment, commercial fishing has great economic importance in some local areas and communities. The value of commercial fishing has been declining, but fishing remains a major component of the region’s recreation and tourism sector. The value of recreational fishing (mostly steelhead) is estimated at $7.7 million annually (1993 dollars). Recreational fishing is enjoyed throughout the basin, particularly downstream of Bonneville Dam. Important localized fisheries occur upstream from Bonneville Dam for fall chinook and for hatchery spring/summer chinook and steelhead. Catch-and-release fisheries for steelhead in some tributaries are also locally important. Furthermore, nonconsumptive fishery-based recreation, such as viewing salmon spawning in rivers and streams, and viewing fish at dams, hatcheries, and fish ladders, generates an estimated $80 million a year in expenditures (Huppert and Fluharty, 1995). In some areas, entire communities, resorts, businesses, and individuals depend heavily on services related to recreational fishing. Salmon Management and Science Identifying appropriate operational responses to facilitate the recovery of salmon populations is a complex scientific and policy task. Dozens of federal, state, and local organizations are responsible for managing the river, its extensive system of dams, and land uses across the watershed. For decades, many scientists

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Managing the Columbia River: Instream Flows, Water Withdrawals, and Salmon Survival and science organizations have investigated the varied aspects of salmon issues. These issues are complicated by the fact that the salmon are anadromous, spending part of their lives in freshwater and part in saltwater. Moreover, the salmon’s habitat extends beyond the Columbia River basin. They pass downstream through the Columbia River estuary, spend one to five years (depending on the species) in marine residence, and then return to their natal streams to spawn. Clear understanding of how additional water withdrawals are likely to affect salmon species and their habitat is thus precluded by many factors. In addition to these factors, smolt (young salmon two or three years old that have acquired a silvery color) survival rates are affected by factors beyond streamflow seasonality and discharge, including water temperature, water chemistry, and changes in both land use and the estuarine environment. Existing scientific research and predictive models provide only partial information on these complex relationships and how they might change in the future. Moreover, there are competing models and paradigms, and not all scientists agree on the fundamental relationships among such parameters as flow, temperature, predation, and salmon survival rates. Several important scientific issues in Columbia River management revolve around the relationships between resident juvenile salmon, smolts, survival rates, and instream flows. These issues are especially important on the middle reach of the river in central Washington, where the Washington State Department of Ecology is responsible for the water rights permitting process. Washington State water law is based on the western U.S. doctrine of prior appropriation, in which water rights are required to make withdrawals. The permitting agency must consider several factors in deciding whether to issue water rights to new, or “junior,” appropriators, including possible impacts of additional withdrawals on federally endangered salmon species. Applicants for new water rights would like to receive permits in order to support economic activities and growth; however, additional withdrawals may negatively affect survival rates of salmon smolts.

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Managing the Columbia River: Instream Flows, Water Withdrawals, and Salmon Survival STUDY BACKGROUND, PROCESS, AND ORGANIZATION The ambiguities and tensions surrounding Columbia River management and science prompted the Washington State Department of Ecology to request assistance from the National Research Council (NRC). The Department of Ecology contacted the NRC in 2002, and later that year the committee that authored this report was appointed. The NRC’s Water Science and Technology Board, working in cooperation with the NRC’s Board on Environmental Studies and Toxicology, appointed the ad hoc Committee on Water Resources Management, Instream Flows, and Salmon Survival in the Columbia River and coordinated the study. The committee conducted its deliberations and its report production in response to the Statement of Task given in Box 1-1. Consistent with the title of the study committee, and consistent with its statement of task, this report emphasizes the implications of water withdrawals from the mainstem Columbia River in the State of Washington (the “middle reach” of the Columbia) for Columbia River salmon. The proposed water extractions considered in this study have the potential to primarily alter two key physical characteristics in the impounded Columbia River as they affect salmon survival—water temperature and water velocity associated with river flow. These factors are of importance to salmonids migrating through the impounded Columbia. Additionally, one salmon species (ocean-type Chinook) spawns and rears in the mainstem Columbia River. This report deals generally with the issues of water withdrawals and instream flow conditions as they affect all Columbia River basin salmon species; but as federally-listed species are a special concern in the basin, parts of the report (e.g., a section of Chapter 4) focus on the effects of future environmental conditions on listed salmon species. Conditions in the river’s tributary streams are also important to salmon survival rates, but given this report’s focus on proposed mainstem water withdrawals, environmental conditions in tributary streams are only of peripheral interest in this study. The report also reviews and comments on several water management scenarios. (These scenarios were presented by the State of Washington and are listed in Appendix A.) This committee held four meetings in 2003. Its first two meetings were in Richland, Washington, in February and in

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Managing the Columbia River: Instream Flows, Water Withdrawals, and Salmon Survival BOX 1-1 Committee on Water Resources Management, Instream Flows, and Salmon Survival in the Columbia River: Statement of Task The committee will assess the risks to salmonids at critical stages in their life cycles under a range of different Columbia River system water management scenarios—including diversions for hydropower and other purposes—under both historical and present hydrological conditions. The study will: Work with a science advisory panel (to be appointed by the Washington Department of Ecology) to gather information necessary to accomplish tasks 3 and 4, from the scientific community with direct experience in the Columbia River Basin, to include holding a workshop in Eastern Washington State. Review and evaluate existing scientific data and analyses related to fish species listed under the Endangered Species Act in the Columbia River basin, as necessary to accomplish tasks 3 and 4. Review and evaluate parameters critical to the survival and recovery of listed fish species as they relate to the hydrology of the Columbia River system in the context of the continued operation of the Federal Columbia River power system and other mainstem power generation facilities. This will include instream flows sufficient for fish and wildlife as well as the potential effects of decreased natural storage capacity on river hydrology. In light of existing withdrawals, describe the risks to salmonid survival of a range of water withdrawals, and the cumulative effects of other factors, during critical times of the salmon life cycle (Note: the State of Washington Department of Ecology suggests an appropriate range of water withdrawals to consider is 250,000 acre-feet to 1,300,000 acre-feet). Evaluate the effects of proposed management criteria, specific diversion quantities, and features of potential water management alternatives (such management information will be provided by the State of Washington). Identify gaps in the knowledge and scientific information that are needed to develop comprehensive strategies for recovering and sustaining listed species and managing water resources to meet human needs.

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Managing the Columbia River: Instream Flows, Water Withdrawals, and Salmon Survival Vancouver, Washington, in March, both of which included presentations from scientists from academia and federal and state agencies, representatives from regional stakeholder groups, basin water managers, and members of the public. At the first two meetings, members of a “Resources Group” (listed in Appendix B), convened by the Department of Ecology to provide scientific input to the study, provided several presentations on key scientific issues. The final two meetings were held in Olympia, Washington, in July and in Washington, D.C., in November, respectively, during which the committee discussed its Statement of Task and prepared its report. In addition to the Resources Group experts, oral and written comments from many interest group representatives and the public were considered. In listening to and discussing comments from all presenters, it became clear that the issue of water withdrawal and management on the Columbia River is both a scientific and a public policy subject of regional as well as national importance. It was concluded that in order to comprehensively address the committee’s task statement, agricultural, biological, cultural, economic, energy, environmental, historical, legal, and political factors all had to be considered. The more important challenge was thus not to decide whether or not to incorporate this diversity of knowledge into this report, but rather how to integrate it in a balanced manner that provided sound advice for managing water resources and salmon in the Columbia River system. The challenges of managing Columbia River water and salmon defy simple solutions, and they are not likely to be successfully resolved with information from a single discipline or by the actions of a single group. Decision makers, scientists, policy analysts, and others must cooperate, as must entities across the basin. This report recommends some changes to water management processes in the basin. Successful implementation will require both cooperation and compromise. This is not to say that cooperation and compromise on Columbia water management issues has been absent, as there is a long history of government scientists working with policy makers on Columbia River water and salmon management issues. The Columbia River basin today, however, may be at a point where novel approaches to collaboration are in order. Humans and society have asked much from the Columbia River, and it has delivered a rich

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Managing the Columbia River: Instream Flows, Water Withdrawals, and Salmon Survival variety of benefits. But after several decades of human and technological interventions on the river and across the basin, the river system has fundamentally changed. In particular, salmon are at a critical point with regard to their long-term survival. If salmon habitat and populations are to be meaningfully protected and restored, people and organizations with stakes in Columbia Basin water may be required to make fundamental adjustments. This report’s organization reflects its multiple perspectives. Following this introductory chapter, Chapter 2 discusses the basin’s broad physical, biological, and social features; Chapter 3 discusses hydrology and water management; Chapter 4 discusses environmental influences on salmon; Chapter 5 discusses laws and institutions; Chapter 6 discusses economics and water management alternatives; Chapter 7 discusses risks and water withdrawals; and Chapter 8 is a brief concluding epilogue. The target audience for this report is broad and includes science and policy experts, public- and private-sector officials, and individual citizens and stakeholder groups in the Columbia River basin in the western United States and Canada. This group includes Canadian and U.S. governors and legislators, tribal leaders, state-level water managers and staff (which includes the State of Washington Department of Ecology), federal agency staff (the Bonneville Power Administration, the Corps of Engineers, the Northwest Power and Conservation Council and its Independent Science Advisory Board, the Columbia Basin Project, NOAA Fisheries, and the U.S. Fish and Wildlife Service), other operators of dams and water diversion structures, Columbia River basin municipalities, farmers, commercial and recreational fishers, foresters, and tourism, recreational, and environmental organizations. Summaries are given at the end of each chapter. The report’s principal conclusions and recommendations are printed in boldface in the Executive Summary and in Chapter 8.