Hydrology, Ecology, and Fishes of the Klamath River Basin

Committee on Hydrology, Ecology, and Fishes of the Klamath River

Board on Environmental Studies and Toxicology

Water Science and Technology Board

Division on Earth and Life Studies

NATIONAL RESEARCH COUNCIL OF THE NATIONAL ACADEMIES

THE NATIONAL ACADEMIES PRESS

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Hydrology, Ecology, and Fishes of the Klamath River Basin Committee on Hydrology, Ecology, and Fishes of the Klamath River Board on Environmental Studies and Toxicology Water Science and Technology Board Division on Earth and Life Studies

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THE NATIONAL ACADEMIES PRESS 500 Fifth Street, NW Washington, DC 20001 NOTICE: The project that is the subject of this report was approved by the Govern- ing Board of the National Research Council, whose members are drawn from the councils of the National Academy of Sciences, the National Academy of Engineer- ing, and the Institute of Medicine. The members of the committee responsible for the report were chosen for their special competences and with regard for appropri- ate balance. This project was supported by Contract No. 05CS811145 between the National Academy of Sciences and the U.S. Bureau of Reclamation. Any opinions, findings, conclusions, or recommendations expressed in this publication are those of the author(s) and do not necessarily reflect the view of the organizations or agencies that provided support for this project. International Standard Book Number-13: 978-0-309-11506-3 (Book) International Standard Book Number-10: 0-309-11506-X (Book) International Standard Book Number-13: 978-0-309-11507-0 (PDF) International Standard Book Number-10: 0-309-11507-8 (PDF) Library of Congress Control Number: 2008921799 Additional copies of this report are available from The National Academies Press 500 Fifth Street, NW Box 285 Washington, DC 20055 800-624-6242 202-334-3313 (in the Washington metropolitan area) http://www.nap.edu Cover: Design by Liza Hamilton, National Research Council. Image of the Klamath River, courtesy of Stephan McMillan (http://www.sonic.net/aquatint/index.html). Copyright 2008 by the National Academy of Sciences. All rights reserved. Printed in the United States of America.

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The National Academy of Sciences is a private, nonprofit, self-perpetuating society of distinguished scholars engaged in scientific and engineering research, dedicated to the furtherance of science and technology and to their use for the general welfare. Upon the authority of the charter granted to it by the Congress in 1863, the Acad- emy has a mandate that requires it to advise the federal government on scientific and technical matters. Dr. Ralph J. Cicerone is president of the National Academy of Sciences. The National Academy of Engineering was established in 1964, under the charter of the National Academy of Sciences, as a parallel organization of outstanding en- gineers. It is autonomous in its administration and in the selection of its members, sharing with the National Academy of Sciences the responsibility for advising the federal government. The National Academy of Engineering also sponsors engineer- ing programs aimed at meeting national needs, encourages education and research, and recognizes the superior achievements of engineers. Dr. Charles M. Vest is presi- dent of the National Academy of Engineering. The Institute of Medicine was established in 1970 by the National Academy of Sciences to secure the services of eminent members of appropriate professions in the examination of policy matters pertaining to the health of the public. The Insti- tute acts under the responsibility given to the National Academy of Sciences by its congressional charter to be an adviser to the federal government and, upon its own initiative, to identify issues of medical care, research, and education. Dr. Harvey V. Fineberg is president of the Institute of Medicine. The National Research Council was organized by the National Academy of Sci- ences in 1916 to associate the broad community of science and technology with the Academy’s purposes of furthering knowledge and advising the federal government. Functioning in accordance with general policies determined by the Academy, the Council has become the principal operating agency of both the National Academy of Sciences and the National Academy of Engineering in providing services to the government, the public, and the scientific and engineering communities. The Coun- cil is administered jointly by both Academies and the Institute of Medicine. Dr. Ralph J. Cicerone and Dr. Charles M. Vest are chair and vice chair, respectively, of the National Research Council. www.national-academies.org

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COMMITTEE ON HYDROLOGY, ECOLOGY, AND FISHES OF THE KLAMATH RIVER Members WILLIAM GRAF (Chair), University of South Carolina, Columbia MICHAEL CAMpANA, Oregon State University, Corvallis GEORGE MATHIAS KONDOLF, University of California, Berkeley JAY LuND, University of California, Davis JuDITH MEYER, University of Georgia, Athens DENNIS MuRpHY, University of Nevada, Reno CHRISTOpHER MYRICK, Colorado State University, Fort Collins TAMMY NEWCOMb, Michigan Department of Natural Resources, Lansing JAYANTHA ObEYSEKERA, South Florida Water Management District, West Palm Beach JOHN pITLICK, University of Colorado, Boulder CLAIR STALNAKER, U.S. Geological Survey (retired), Fort Collins, CO GREGORY WILKERSON, University of Illinois, Urbana pRzEMYSLAW (ANDY) zIELINSKI, Ontario Power Generation, Toronto Staff DAVID pOLICANSKY, Study Director SuzANNE VAN DRuNICK, Senior Program Officer LAuREN ALExANDER, Senior Program Officer RuTH CROSSGROVE, Senior Editor MIRSADA KARALIC-LONCAREVIC, Manager of the Technical Information Center JORDAN CRAGO, Senior Project Assistant RADIAH ROSE, Senior Editorial Assistant Sponsor u.S. buREAu RECLAMATION OF v

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bOARD ON ENVIRONMENTAL STuDIES AND TOxICOLOGY Members JONATHAN M. SAMET (Chair), Johns Hopkins University, Baltimore, MD RAMóN ALVAREz, Environmental Defense, Austin, TX JOHN M. bALbuS, Environmental Defense, Washington, DC DALLAS buRTRAW, Resources for the Future, Washington, DC JAMES S. buS, Dow Chemical Company, Midland, MI RuTH DEFRIES, University of Maryland, College Park COSTEL D. DENSON, University of Delaware, Newark E. DONALD ELLIOTT, Willkie Farr & Gallagher LLP, Washington, DC MARY R. ENGLISH, University of Tennessee, Knoxville J. pAuL GILMAN, Oak Ridge Center for Advanced Studies, Oak Ridge, TN SHERRI W. GOODMAN, Center for Naval Analyses, Alexandria, VA JuDITH A. GRAHAM, American Chemistry Council, Arlington, VA WILLIAM p. HORN, Birch, Horton, Bittner and Cherot, Washington, DC WILLIAM M. LEWIS, JR., University of Colorado, Boulder JuDITH L. MEYER, University of Georgia, Athens DENNIS D. MuRpHY, University of Nevada, Reno pATRICK Y. O’bRIEN, ChevronTexaco Energy Technology Company, Richmond, CA DOROTHY E. pATTON (retired), Chicago, IL DANNY D. REIbLE, University of Texas, Austin JOSEpH V. RODRICKS, ENVIRON International Corporation, Arlington, VA ARMISTEAD G. RuSSELL, Georgia Institute of Technology, Atlanta RObERT F. SAWYER, University of California, Berkeley KIMbERLY M. THOMpSON, Massachusetts Institute of Technology, Cambridge MONICA G. TuRNER, University of Wisconsin, Madison MARK J. uTELL, University of Rochester Medical Center, Rochester, NY CHRIS G. WHIppLE, ENVIRON International Corporation, Emeryville, CA LAuREN zEISE, California Environmental Protection Agency, Oakland Senior Staff JAMES J. REISA, Director DAVID J. pOLICANSKY, Scholar RAYMOND A. WASSEL, Senior Program Officer for Environmental Sciences and Engineering EILEEN N. AbT, Senior Program Officer for Risk Analysis vi

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SuSAN N.J. MARTEL, Senior Program Officer for Toxicology KuLbIR bAKSHI, Senior Program Officer KARL E. GuSTAVSON, Senior Program Officer ELLEN K. MANTuS, Senior Program Officer RuTH E. CROSSGROVE, Senior Editor vii

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WATER SCIENCE AND TECHNOLOGY bOARD Members CLAIRE WELTY, Chair, University of Maryland, Baltimore County JOAN G. EHRENFELD, Rutgers University, New Brunswick, NJ SIMON GONzALEz, National Autonomous University of Mexico, Mexico City CHARLES N. HAAS, Drexel University, Philadelphia, PA JAMES M. HuGHES, Emory University, Atlanta, GA THEODORE L. HuLLER, Cornell University, Ithaca, NY KIMbERLY L. JONES, Howard University, Washington, DC G. TRACY MEHAN III, The Cadmus Group, Inc., Arlington, VA JAMES K. MITCHELL, Virginia Polytechnic Institute and State University, Blacksburg DAVID H. MOREAu, University of North Carolina, Chapel Hill LEONARD SHAbMAN, Resources for the Future, Washington, DC DONALD I. SIEGEL, Syracuse University, Syracuse, NY SOROOSH SOROOSHIAN, University of California, Irvine HAME M. WATT, Independent Consultant, Washington, DC JAMES L. WESCOAT, JR., University of Illinois at Urbana-Champaign GARRET p. WESTERHOFF, Malcolm Pirnie, Inc., White Plains, NY Staff STEpHEN D. pARKER, Director LAuREN E. ALExANDER, Senior Staff Officer LAuRA J. EHLERS, Senior Staff Officer JEFFREY W. JACObS, Senior Staff Officer STEpHANIE E. JOHNSON, Senior Staff Officer WILLIAM S. LOGAN, Senior Staff Officer M. JEANNE AquILINO, Financial and Administrative Associate ANITA A. HALL, Administrative Assistant ELLEN A. DE GuzMAN, Senior Program Associate DOROTHY K. WEIR, Research Associate viii

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OTHER REpORTS OF THE bOARD ON ENVIRONMENTAL STuDIES AND TOxICOLOGY Models in Environmental Regulatory Decision Making (2007) Toxicity Testing in the Twenty-first Century: A Vision and a Strategy (2007) Sediment Dredging at Superfund Megasites: Assessing the Effectiveness (2007) Environmental Impacts of Wind-Energy Projects (2007) Scientific Review of the Proposed Risk Assessment Bulletin from the Office of Management and Budget (2007) Assessing the Human Health Risks of Trichloroethylene: Key Scientific Issues (2006) New Source Review for Stationary Sources of Air Pollution (2006) Human Biomonitoring for Environmental Chemicals (2006) Health Risks from Dioxin and Related Compounds: Evaluation of the EPA Reassessment (2006) Fluoride in Drinking Water: A Scientific Review of EPA’s Standards (2006) State and Federal Standards for Mobile-Source Emissions (2006) Superfund and Mining Megasites—Lessons from the Coeur d’Alene River Basin (2005) Health Implications of Perchlorate Ingestion (2005) Air Quality Management in the United States (2004) Endangered and Threatened Species of the Platte River (2004) Atlantic Salmon in Maine (2004) Endangered and Threatened Fishes in the Klamath River Basin (2004) Cumulative Environmental Effects of Alaska North Slope Oil and Gas Development (2003) Estimating the Public Health Benefits of Proposed Air Pollution Regulations (2002) Biosolids Applied to Land: Advancing Standards and Practices (2002) The Airliner Cabin Environment and Health of Passengers and Crew (2002) Arsenic in Drinking Water: 2001 Update (2001) Evaluating Vehicle Emissions Inspection and Maintenance Programs (2001) Compensating for Wetland Losses Under the Clean Water Act (2001) A Risk-Management Strategy for PCB-Contaminated Sediments (2001) Acute Exposure Guideline Levels for Selected Airborne Chemicals (five volumes, 2000-2007) Toxicological Effects of Methylmercury (2000) ix

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Strengthening Science at the U.S. Environmental Protection Agency (2000) Scientific Frontiers in Developmental Toxicology and Risk Assessment (2000) Ecological Indicators for the Nation (2000) Waste Incineration and Public Health (2000) Hormonally Active Agents in the Environment (1999) Research Priorities for Airborne Particulate Matter (four volumes, 1998-2004) The National Research Council’s Committee on Toxicology: The First 50 Years (1997) Carcinogens and Anticarcinogens in the Human Diet (1996) Upstream: Salmon and Society in the Pacific Northwest (1996) Science and the Endangered Species Act (1995) Wetlands: Characteristics and Boundaries (1995) Biologic Markers (five volumes, 1989-1995) Review of EPA’s Environmental Monitoring and Assessment Program (three volumes, 1994-1995) Science and Judgment in Risk Assessment (1994) Pesticides in the Diets of Infants and Children (1993) Dolphins and the Tuna Industry (1992) Science and the National Parks (1992) Human Exposure Assessment for Airborne Pollutants (1991) Rethinking the Ozone Problem in Urban and Regional Air Pollution (1991) Decline of the Sea Turtles (1990) Copies of these reports may be ordered from the National Academies Press (800) 624-6242 or (202) 334-3313 www.nap.edu x

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OTHER REpORTS OF THE WATER SCIENCE AND TECHNOLOGY bOARD Colorado River Basin Water Management: Evaluating and Adjusting to Hydroclimatic Variability (2007) Improving the Nation’s Water Security: Opportunities for Research (2007) CLEANER and NSF’s Environmental Observatories (2006) Drinking Water Distribution Systems: Assessing and Reducing Risks (2006) Progress Toward Restoring the Everglades: The First Biennial Review, 2006 (2006) River Science at the U.S. Geological Survey (2006) Second Report of the National Academy of Engineering/National Research Council Committee on New Orleans Regional Hurricane Protection Projects (2006) Structural Performance of the New Orleans Hurricane Protection System During Hurricane Katrina: Letter Report (2006) Third Report of the NAE/NRC Committee on New Orleans Regional Hurricane Protection Projects (2006) Toward a New Advanced Hydrologic Prediction Service (AHPS) (2006) Public Water Supply Distribution Systems: Assessing and Reducing Risks (2005) Re-engineering Water Storage in the Everglades: Risks and Opportunities (2005) Regional Cooperation for Water Quality Improvement in Southwestern Pennsylvania (2005) Review of the Lake Ontario-St. Lawrence River Studies (2005) Science of Instream Flows: A Review of the Texas Instream Flow Program (2005) Water Conservation, Reuse, and Recycling (2005) Water Resources Planning for the Upper Mississippi River and Illinois Waterway (2005) Adaptive Management for Water Resources Project Planning (2004) Analytical Methods and Approaches for Water Resources Project Planning (2004) Army Corps of Engineers Water Resources Planning: A New Opportunity for Service (2004) Assessing the National Streamflow Information Program (2004) Confronting the Nation’s Water Problems: The Role of Research (2004) Contaminants in the Subsurface: Source Zone Assessment and Remediation (2004) Groundwater Fluxes Across Interfaces (2004) Managing the Columbia River: Instream Flows, Water Withdrawals, and Salmon Survival (2004) xi

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Review of the Desalination and Water Purification Technology Roadmap (2004) Review of U.S. Army Corps of Engineers Upper Mississippi River-Illinois Waterway Restructured Feasibility Study (2004) U.S. Army Corps of Engineers Water Resources Project Planning: A New Opportunity for Service (2004) Valuing Ecosystem Services: Toward Better Environmental Decision- Making (2004) Adaptive Monitoring and Assessment for the Comprehensive Everglades Restoration Plan (2003) Does Water Flow Influence Everglades Landscape Patterns? (2003) Environmental Cleanup at Navy Facilities: Adaptive Site Management (2003) Review of the EPA Water Security Research and Technical Support Action Plan (2003) Review of the EPA Water Security Research and Technical Support Action Plan: Part 2. Project Evaluation (2003) Bioavailability of Contaminants in Soils and Sediments: Processes, Tools, and Applications (2002) Estimating Water Use in the United States: A New Paradigm for the National Water-Use Information Program (2002) Florida Bay Research Programs and Their Relation the Comprehensive Everglades Restoration Plan (2002) The Missouri River Ecosystem: Exploring the Prospects of Recovery (2002) Opportunities to Improve the USGS National Water Quality Assessment Program (2002) Privatization of Water Services in the United States: An Assessment of Issues and Experience (2002) Report of a Workshop on Predictability and Limits-to-Prediction in Hydrologic Systems (2002) Review of the Florida Keys Carrying Capacity Study, A (2002) Review of the USGCRP Plan for a New Scientific Initiative on Global Water Cycle (2002) Riparian Areas: Functions and Strategies for Management (2002) Arsenic in Drinking Water (2001) Assessing the Total Maximum Daily Load Approach to Water Quality Management (2001) Copies of these reports may be ordered from the National Academies Press (800) 624-6242 or (202) 334-3313 www.nap.edu xii

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Preface The Klamath River basin is both at the edge and at the center. The basin is a 15,700 square mile watershed at the western rim of North America, where it encompasses a diverse ecosystem, wilderness areas, and irrigated farmlands in southern Oregon and Northern California. The basin is lo- cated at the center, however, of the landscape of controversy in American environmental management, and the issues that face Klamath River basin decision makers exemplify in magnified form many of the difficult science and policy challenges that have arisen across the continent. Management of the basin’s hydrologic and ecological resources is complicated because deci- sion makers must sort through a myriad of potential strategies for operat- ing a complex system with interrelated rivers, lakes, marshes, dams, and diversions. The river basin boundaries outline an ecosystem that includes economically valuable water resources and ecologically valuable species, including endangered, threatened, and other fishes, which are dependent on the rivers and lakes for their survival. Alterations to the original hydrologic system began in the late 1800s, accelerated in the early 1900s, and continue today. They include water-control works by private land and water own- ers, by the large and intricate Klamath Irrigation Project of the U.S. Bureau of Reclamation (USBR), and by several hydroelectric dams operated by a private corporation, PacifiCorp. These hydrologic alterations, combined with overfishing, habitat al- teration, poor water quality, and nonnative species, have led to a dramatic decline in coho salmon, Lost River suckers, and short-nose suckers and some other fishes of the Klamath River. Salmon, once providing the basis of the third largest salmon fishery among west-coast rivers, are a critical xiii

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xiv PREFACE component of the ecosystems and cultural systems of the Klamath region. By the end of the twentieth century, the inherent difficulties in balancing the benefits of the river’s water for fish, agriculture, and hydropower had become further complicated by national resource policies supporting Native American rights, water development, hydropower production, and endan- gered and threatened species. Science and engineering have been the handmaidens of water develop- ment in the Klamath River basin, and decision makers have called upon science and engineering expertise to aid them in sorting out the choices for future management of the basin’s water and water-related resources. Rec- ognizing that the best decisions are likely to benefit from the understanding derived from scientific research and engineering investigations, in 2001 the U.S. Department of Interior and the U.S. Department of Commerce requested that the National Research Council (NRC) form a committee to complete two reports. The first (interim) study, completed in 2002, as- sessed the strength of scientific support for the 2001 biological assessments and biological opinions on the three endangered or threatened fish species in the Klamath River basin. The second (final) study, completed in 2004, evaluated the 2002 biological assessments and biological opinions, and other matters related to the long-term survival and recovery of the federally listed fish species. Subsequently, in 2005 the Bureau of Indian Affairs (on behalf of the Native American tribes of the basin) and the USBR (serving many irrigators in the basin) requested that the NRC conduct a more specific evaluation and review two new studies, completed after 2004, which were designed to inform decision makers about the hydrology and fish ecology of the Klamath River basin. In order to define hydrologic conditions that sup- ported the predevelopment fish population, one study used data and model- ing approaches to gain an understanding of what the natural flows of the river might be without the presence of agriculture and the water control infrastructure. The second study created a model-based linkage between the hydrology and the resulting aquatic ecosystems that support the fish popu- lations in the river. The present report is the outcome of the NRC review and evaluation of those studies. The committee is grateful for the support of USBR officials Pablo Ar- royave, William Rinne, James Hess, and William Shipp. Many people with close associations with the Klamath River basin aided the committee in its efforts to understand the Klamath River basin and its resources. The people of Yreka, California, and Klamath Falls, Oregon, made the com- mittee welcome and shared their perspectives during committee visits to those communities. During public sessions associated with those visits, local citizens joined federal, state, and local agency representatives in discussions and presentations for the committee. Jon Hicks and Cindy Williams, of the

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xv PREFACE USBR’s Klamath Falls Office, were particularly helpful to the committee in gaining an understanding of the Klamath Project, a key component of the present basin system. During a visit by some committee and staff members to Utah State University in Logan, Dr. Thomas Hardy extended every courtesy, as did Craig Albertson, Elizabeth Cohen, Alan Harrison, Thomas Perry, and Mark Spears during another similar visit to the USBR offices in Denver, Colorado. These researchers repeatedly aided the committee in tracking down information, data, and elusive documents. The committee also benefited from terrific support from the NRC staff. James Reisa (director of the Board on Environmental Studies and Toxicology) and Stephen Parker (director of the Water Science and Technology Board) provided a supportive institutional home for the committee and its members. David Policansky (scholar and senior program officer of the Board on Envi- ronmental Studies and Toxicology) played a pivotal role in the deliberations of the committee and the writing of the report. His wide experience, range of knowledge, and congenial interactions with the committee were important contributions to the result. Suzanne van Drunick (project director and senior program officer) guided the committee with great wisdom and adroit man- agement through its meetings and its report writing, providing organizational skills and knowledge of the Klamath issues that made the report possible. The extensive hydrologic knowledge and sound judgment of Lauren Alexander (senior staff officer of the Water Science and Technology Board) contributed substantially to early stages of development of the committee and its report. The complicated mechanics of arrangements for committee meetings and travel, as well as the smooth production of the meetings was in the capable hands of senior program assistants Liza Hamilton and Jordan Crago. Ruth Crossgrove did her usual scholarly job of editing the report. Thank you to all of these talented NRC professionals. This report is the consensus expression of the committee’s conclusions and recommendations, but it is actually the product of hard work and thoughtful review. We express our appreciation to members of the Board on Environmental Studies and Toxicology and the Water Science Board; to the NRC’s Report Review Committee, which took on the responsibility of external review oversight; and to the independent scientists and engineers listed below, who reviewed the report. These reviewers provided us with insightful commentary, numerous penetrating questions, and exceptionally helpful suggestions for clarifying and improving our report. We benefited enormously from their help. This report has been reviewed in draft form by individuals chosen for their diverse perspectives and technical expertise, in accordance with pro- cedures approved by the NRC’s Report Review Committee. The purpose of this independent review is to provide candid and critical comments that will assist the institution in making its published report as sound as possible

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xvi PREFACE and to ensure that the report meets institutional standards of objectivity, evidence, and responsiveness to the study charge. The review comments and draft manuscript remain confidential to protect the integrity of the deliberative process. We thank the following individuals for their review of this report: Stanley Gregory, Oregon State University Robert Huggett, Seaford, Virginia William Lewis, University of Colorado David Maidment, University of Texas Jeffrey Mount, University of California at Davis Patrick O’Brien, ChevronTexaco Energy Technology Company LeRoy Poff, Colorado State University Gordon Robilliard, Entrix, Inc. Kenneth Rykbost, Klamath Falls, Oregon Although the reviewers listed above have provided many constructive comments and suggestions, they were not asked to endorse the conclusions or recommendations, nor did they see the final draft of the report before its release. The review of this report was overseen by the review coordina- tor, Paul G. Risser, of Oklahoma State University, and the review monitor, Gordon H. Orians, of the University of Washington (emeritus). Appointed by the NRC, they were responsible for making certain that an independent examination of this report was carried out in accordance with institutional procedures and that all review comments were carefully considered. Re- sponsibility for the final content of this report rests entirely with the author- ing committee and the institution. To my fellow committee members, I express a special debt of gratitude. They were a committee drawn from different backgrounds and disciplinary cultures, yet they were willing to work together in a harmonious collective effort to address the complexities of science and engineering for the Klam- ath River system. They put aside their personal biases, worked long hours that sacrificed their own professional time, and traveled great distances to make their contributions to this report. Such unpaid service is remarkable, but the committee received a truly remarkable recompense: the opportunity to contribute the experience and knowledge collected from our careers to support a public vision for the future of the basin and its resources. It is our hope that, although the Klamath River basin is at the edge of the continent, it will also be a central example of successful application of science and engineering to American ecosystem restoration and management. William L. Graf, Chair Committee on Hydrology, Ecology, and Fishes of the Klamath River Basin

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Contents SUMMARY 3 1 INTRODUCTION 16 The Klamath River Basin, 16 Recent History, 20 The Present Study, 23 Report Organization, 24 2 THE KLAMATH BASIN 25 Description of the Basin, 25 Human-Induced Changes in the Basin, 41 Summary, 49 3 FORMULATING AND APPLYING MODELS IN ECOSYSTEM MANAGEMENT 53 Introduction, 53 Types of Models and Modeling Areas, 58 The Modeling Process, 77 Institutional Models for Integrating Knowledge and Management, 85 Conclusions, 90 4 NATURAL FLOW STUDY 91 Introduction, 91 Methods for the Natural Flow Study, 99 xvii

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xviii CONTENTS Data for the Natural Flow Study, 111 Alternative Approaches and Follow-up, 122 The Natural Flow Model: Consequences, 128 Conclusions and Recommendations, 129 Management Implications of the Natural Flow Study, 132 5 INSTREAM FLOW STUDY 135 Technical Elements of an Instream Flow Study, 135 Overview of Procedures Used in the Instream Flow Study, 146 Evaluation of Phase II Instream Flow Study, 163 Implications for Implementing Flow Recommendations, 180 Comprehensive Analyses and Integration, 186 Conclusions and Recommendations, 188 Management Implications of the Instream Flow Study, 194 6 APPLYING SCIENCE TO MANAGEMENT 196 Introduction, 196 Adaptive Management, 197 Conclusions and Recommendations, 209 Summary, 209 7 CONCLUSIONS AND RECOMMENDATIONS 211 The Big Picture, 211 Four Major Themes, 213 Natural Flow Study, 215 Instream Flow Study, 218 What Is the Utility of the Two Studies for Decision Making? 223 Connecting Science with Decision Making, 224 REFERENCES 226 APPENDIX: BIOGRAPHICAL INFORMATION FOR COMMITTEE MEMBERS 243 bOxES, TAbLES, AND FIGuRES BOXES 5-1 Critical Methodological Issues for the Analysis of Habitat-Instream Flow Relationships, 146

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xix CONTENTS TABLES 2-1 Klamath Basin Sub-basins Shown in Figure 2-2, 26 2-2 Native Fishes of the Lower Klamath River and Its Tributaries and Their Status, 33 2-3 Chinook Salmon, Coho Salmon, and Steelhead Life Periodicities Between Iron Gate Dam and the Trinity River, 36 2-4 Native and Nonnative Fishes of the Upper Klamath Basin and Their Status, 37 2-5 Species Life Stages and Concerns for Management As Noted by Month, 40 2-6 A Sampling of the Many Government Agencies, Stakeholder Organizations, and Working Groups in the Klamath Basin, 42 2-7 Overview of the Habitat Factors Considered Important in the Decline in Anadromous Fish Populations and Their Potential Impacts, 50 3-1 Adjectives Used to Classify Hydrologic Models, 60 3-2 Models for Coupling with the USGS Three-Dimensional (3-D) Groundwater Model MODFLOW, 61 5-1 Flow Regime Components and Their Effect on Physical Processes, Biological Processes, and Water Quality, 138 5-2 Testing of Habitat-Suitability Model Results, 179 FIGURES 1-1 Map of the upper Klamath River basin showing surface waters and landmarks mentioned in this report, 17 1-2 Iron Gate Dam on the Klamath River is the dividing point between the upper and lower Klamath River basins, 18 1-3 A short reach of the lower Klamath River near Gottsville, California, shows the complexity of the channel and the variety of aquatic habitats in the stream, 19 1-4 Chart of recent history of events in the Klamath basin related to threatened and endangered fishes, 22 2-1 Land use throughout the Klamath basin divided into sub-basins, 27 2-2a This reach of the Link River below Upper Klamath Lake, shown here in 1919, is the site of Link River Dam, 29 2-2b The newly completed Link River Dam spans the channel and diverts much of the river’s discharge into the Keno Canal on the right bank in this 1922 image made from the same location as in Figure 2-2a, 29

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xx CONTENTS 2-2c The Link River Dam, shown from the same location as in Figures 2-2 a and b, diverts water into the Keno Canal and the Ankeny Canal in this view made about 1940, 30 2-2d The Link River Dam, shown in this 2006 view from the same location as the views in Figures 2-2 a, b, and c, now includes a fish ladder, recently installed near the right abutment (left side of the dam in this image), 30 2-3 Conceptual model of the sediment transport and channel geomorphology in the Klamath River in the reaches affected by the PacifiCorp hydroelectric project dams, 45 2-4 Spawning Chinook salmon, 1978-2006, 49 3-1 Conceptual model of the Central Valley, California. Diversions include diversions for agriculture, 56 3-2 The Grand Canyon Ecosystem Model, 57 3-3 Conceptual watershed system represented in PRMS, 62 3-4 Schematic representation of a watershed in MIKE-SHE model, 63 3-5 Conceptual illustration of the variety of factors important in controlling salmon production throughout SALMOD’s biological year, 70 3-6 Interactions among models to represent an ecosystem and its management, 71 3-7 Standard modeling protocols, 79 4-1 Keno Dam rests atop a bedrock sill across the Klamath River near Keno, Oregon, 92 4-2 The U.S. Geological Survey stream gauge site on the Klamath River immediately below Iron Gate Dam is the site for calculated natural flows and recommended instream flows, 93 4-3 Conceptual model of the NFS, 98 4-4 Flowchart of natural stream flow methods used for computing natural inflows to Upper Klamath Lake, 101 4-5 Agriculture is an important economic activity in the upper Klamath basin, 103 4-6 The NFS adjusted flows from the upper Klamath River basin to account for the conversion of marsh areas to agriculture, such as shown here on the southeast side of Upper Klamath Lake, 104 4-7 Comparison of Kimberly-Penman evapotranspiration estimates for alfalfa reported for KFLO AgriMet station (box-whisker plots) with the evapotranspiration estimates of Cuenca et al. (1992, p. 128): (a) evapotranspiration values corresponding to 19 out of 20 years; and (b) evapotranspiration values corresponding to 5 out of 10 years, 106

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xxi CONTENTS 4-8 Climatic spells identified from precipitation records at Yreka and Klamath Falls and from Upper Klamath Lake net inflow time series, 112 4-9 Cumulative departure from average precipitation for Climate Division 5 of Oregon and Climate Division 1 of California, 113 4-10 Annual precipitation data for (A) Climate Division 5 of Oregon and (B) Climate Division 1 of California for the periods 1895-1948 and 1949-2000, 115 4-11 Average annual stream flow of the Williamson River below the Sprague River near Chiloquin, Oregon, 1918-2005, USGS gauge, 116 4-12 Cumulative departures in annual precipitation in Oregon Climate Division 5 and at Crater Lake, Oregon, and annual discharge for the Williamson River below the Sprague River, 117 4-13 Measured (gauged) flow plotted as a percentage of the estimated natural flow, 118 4-14 NARR grid points near Upper Klamath Lake used for downloading climatic data for evapotranspiration estimation, 126 4-15 Box and whisker plots of monthly evapotranspiration (summed from daily data) estimated by using the NARR meteorological data for grid point number 5 (Figure 4-14) and the Penman- Monteith equation, 127 5-1 Illustration depicting flow regime components (subsistence flow, base flow, overbank, high-flow pulse), 136 5-2 Overall data flow diagram of field data collection step in the Phase II study of the IFS, 149 5-3 This reach of the Klamath River between Iron Gate Dam and the abandoned settlement of Klamathon is typical of the representative reaches used in the IFS, 150 5-4 Estimated mean monthly flows and observed flows (1961-2000) at Iron Gate Dam, 152 5-5 Annual flow duration plots at Iron Gate for the observed and estimated flows based on the USBR NFS and level-pool, consumptive-use-based methods, 153 5-6 Overall data flow diagram of the hydrodynamic and hydrologic modeling step in the IFS Phase II study, 154 5-7 Overall data flow diagram of the habitat-suitability criteria development and validation step in the IFS Phase II study, 157 5-8 Overall data flow diagram of the habitat modeling step in the IFS Phase II study, 158

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xxii CONTENTS 5-9 Overall data flow diagram of instream flow recommendation and justification step in the IFS Phase II study, 159 5-10 Mean daily and monthly flow of the Klamath River below Iron Gate Dam and Williamson River near Chiloquin in a year of near-average water availability, 165 5-11 Comparison of monthly flows for Klamath River below Iron Gate Dam based on the NFS, 184 5-12 Comparison of modified Table 9 flows (NMFS 2002; USGS 2005) with Hardy et al. (2006a) instream flow recommendations, 185 5-13 Relationship between October-March precipitation and naturalized flows at Iron Gate Dam during April-September period, 186 6-1 Flow diagram for adaptive management of scientific activities, 199 6-2 Organizational charts of four adaptively managed restoration programs, 204