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Endangered and Threatened Fishes in the Klamath River Basin: Causes of Decline and Strategies for Recovery (2004)

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ISBN 978-0-309-09097-1 | DOI 10.17226/10838

Committee on Endangered and Threatened Fishes in the Klamath River Basin; Board on Environmental Studies and Toxicology; Division on Earth and Life Studies;

National Research Council

National Research Council. 2004. Endangered and Threatened Fishes in the Klamath River Basin: Causes of Decline and Strategies for Recovery.

Washington, DC: The National Academies Press. https://doi.org/10.17226/10838.

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Endangered and Threatened Fishes in the Klamath River Basin: Causes of Decline and Strategies for ...

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Committee on Endangered and Threatened Fishes in the Klamath River Basin

Board on Environmental Studies and Toxicology

Division on Earth and Life Studies

ENDANGERED AND

THREATENED FISHES

IN THE KLAMATH

RIVER BASIN

CAUSES OF DECLINE AND STRATEGIES FOR RECOVERY

https://nap.nationalacademies.org/catalog/10838?s=z1120

Endangered and Threatened Fishes in the Klamath River Basin: Causes of Decline and Strategies for ...

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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 appropriate balance.

This project was supported by Grant 98210-1-G092 between the National Academy of Sciences and the U.S. Department of the Interior and the U.S. Depart-ment of Commerce. Any opinions, findings, conclusions, or recommendations ex-pressed in this publication are those of the authors and do not necessarily reflect the view of the organizations or agencies that provided support for this project.

Library of Congress Cataloging-in-Publication Data

Endangered and threatened fishes in the Klamath River Basin : causes of decline and strategies for recovery.

p. cm.

Includes bibliographical references (p. ).

ISBN 0-309-09097-0 (hardcover) — ISBN 0-309-52808-9 (pdf)

1. Rare fishes—Klamath River Watershed (Or. and Calif.) 2. Fishes—Conserva-tion—Klamath River Watershed (Or. and Calif.) I. National Academies Press (U.S.).

QL617.73.U6E53 2004

333.95′68′09795—dc22 2004001241

Cover illustration by Janice C. Fong, University of California, Davis; copyright 2004.

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Endangered and Threatened Fishes in the Klamath River Basin: Causes of Decline and Strategies for ...

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Endangered and Threatened Fishes in the Klamath River Basin: Causes of Decline and Strategies for ...

Endangered and Threatened Fishes in the Klamath River Basin: Causes of Decline and Strategies for ...

v

COMMITTEE ON ENDANGERED AND THREATENED FISHES

IN THE KLAMATH RIVER BASIN

Members WILLIAM M. LEWIS, JR. (Chair), University of Colorado, Boulder RICHARD M. ADAMS, Oregon State University, Corvallis ELLIS B. COWLING, North Carolina State University, Raleigh EUGENE S. HELFMAN, University of Georgia, Athens CHARLES D. D. HOWARD, Consulting Engineer, Victoria, British Columbia, Canada ROBERT J. HUGGETT, Michigan State University, East Lansing NANCY E. LANGSTON, University of Wisconsin, Madison JEFFREY F. MOUNT, University of California, Davis PETER B. MOYLE, University of California, Davis TAMMY J. NEWCOMB, Michigan Department of Natural Resources, Lansing MICHAEL L. PACE, Institute of Ecosystem Studies, Millbrook, NY J.B. RUHL, Florida State University, Tallahassee

Staff SUZANNE VAN DRUNICK, Project Director DAVID J. POLICANSKY, Associate Director and Senior Program Director for

Applied Ecology NORMAN GROSSBLATT, Senior Editor KELLY CLARK, Assistant Editor MIRSADA KARALIC-LONCAREVIC, Research Assistant BRYAN P. SHIPLEY, Research Assistant

Sponsors

U.S. DEPARTMENT OF THE INTERIOR

U.S. DEPARTMENT OF COMMERCE

Endangered and Threatened Fishes in the Klamath River Basin: Causes of Decline and Strategies for ...

vi

BOARD ON ENVIRONMENTAL STUDIES AND TOXICOLOGY1

Members JONATHAN M. SAMET (Chair), Johns Hopkins University, Baltimore, MD DAVID ALLEN, University of Texas, Austin THOMAS BURKE, Johns Hopkins University, Baltimore, MD JUDITH C. CHOW, Desert Research Institute, Reno, NV COSTEL D. DENSON, University of Delaware, Newark E. DONALD ELLIOTT, Wilkie, Farr & Galagher, LLP, Washington, DC CHRISTOPHER B. FIELD, Carnegie Institute of Washington, Stanford, CA WILLIAM H. GLAZE, Oregon Health and Science University, Beaverton SHERRI W. GOODMAN, Center for Naval Analyses, Alexandria, VA DANIEL S. GREENBAUM, Health Effects Institute, Cambridge, MA ROGENE HENDERSON, Lovelace Respiratory Research Institute, Albuquerque, NM CAROL HENRY, American Chemistry Council, Arlington, VA ROBERT HUGGETT, Michigan State University, East Lansing BARRY L. JOHNSON, Emory University, Atlanta, GA JAMES H. JOHNSON, Howard University, Washington, DC JUDITH L. MEYER, University of Georgia, Athens PATRICK Y. O’BRIEN, ChevronTexaco Energy Technology Company, Richmond, CA DOROTHY E. PATTON, International Life Sciences Institute, Washington, DC STEWARD T. A. PICKETT, Institute of Ecosystem Studies, Millbrook, NY ARMISTEAD G. RUSSELL, Georgia Institute of Technology, Atlanta LOUISE M. RYAN, Harvard University, Boston, MA KIRK SMITH, University of California, Berkeley LISA SPEER, Natural Resources Defense Council, New York, NY G. DAVID TILMAN, University of Minnesota, St. Paul CHRIS G. WHIPPLE, Environ Incorporated, Emeryville, CA LAUREN A. ZEISE, California Environmental Protection Agency, Oakland, CA

Senior Staff JAMES J. REISA, Director DAVID J. POLICANSKY, Associate Director RAYMOND A. WASSEL, Senior Program Director for Environmental Sciences and Engineering KULBIR BAKSHI, Program Director for the Committee on Toxicology ROBERTA M. WEDGE, Program Director for Risk Analysis K. JOHN HOLMES, Senior Staff Officer SUSAN N. J. MARTEL, Senior Staff Officer SUZANNE VAN DRUNICK, Senior Staff Officer EILEEN N. ABT, Senior Staff Officer ELLEN K. MANTUS, Senior Staff Officer RUTH E. CROSSGROVE, Managing Editor

1This study was planned, overseen, and supported by the Board on Environmental Studies and Toxicology.

Endangered and Threatened Fishes in the Klamath River Basin: Causes of Decline and Strategies for ...

vii

OTHER REPORTS OF THE BOARD ON ENVIRONMENTAL

STUDIES AND TOXICOLOGY

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) Ecological Dynamics on Yellowstone’s Northern Range (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

(3 volumes; 2000–2003) Toxicological Effects of Methylmercury (2000) 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) Modeling Mobile-Source Emissions (2000) Waste Incineration and Public Health (1999) Hormonally Active Agents in the Environment (1999) Research Priorities for Airborne Particulate Matter (4 volumes, 1998–2003) Ozone-Forming Potential of Reformulated Gasoline (1999) Arsenic in Drinking Water (1999) 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 (5 volumes, 1989–1995) Review of EPA’s Environmental Monitoring and Assessment Program

(3 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)

Endangered and Threatened Fishes in the Klamath River Basin: Causes of Decline and Strategies for ...

viii

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

Endangered and Threatened Fishes in the Klamath River Basin: Causes of Decline and Strategies for ...

ix

This project was supported by the U.S. Bureau of Reclamation (USBR), the U.S. Fish and Wildlife Service (USFWS), and the National Marine Fish-eries Service (NMFS).

Many people assisted the committee and National Research Council staff in creating this report. We are grateful for the support provided by the following:

Pablo Arroyave, U.S. Bureau of Reclamation Edward Bartell, Water for Life Foundation John Bartholow, U.S. Geological Survey Michael Belchik, Yurok Tribe Antonio Bentivoglio, U.S. Fish and Wildlife Service Gary Black, Siskiyou Resource Conservation District Randy Brown, U.S. Fish and Wildlife Service Mark Buettner, U.S. Fish and Wildlife Service Donald Buth, University of California, Los Angeles James Carpenter, Carpenter Design Inc.

William Chesney, California Department of Fish and Game Paul Cleary, Oregon Department of Water Resources David Cottingham, Marine Mammal Commission John Crawford, Tule Lake Irrigation District Earl Danosky, Tule Lake Irrigation District Michael Deas, Watercourse Engineering Inc.

Thomas Dowling, Arizona State University Larry Dunsmoor, Klamath Tribes Natural Resources

Acknowledgments

Endangered and Threatened Fishes in the Klamath River Basin: Causes of Decline and Strategies for ...

x ACKNOWLEDGMENTS

John Fay, U.S. Fish and Wildlife Service Mary Freeman, U.S. Geological Survey Thomas Hardy, Utah Water Research Laboratory William Hogarth, National Marine Fisheries Service Becky Hyde, Yainex Ranch Owner Cecil Jennings, U.S. Geological Survey Marshall Jones, U.S. Fish and Wildlife Service John Keys, III, U.S. Bureau of Reclamation Jacob Kann, Aquatic Ecosystem Sciences LLC Steve Kirk, Oregon Department of Environmental Quality Don Knowles, National Marine Fisheries Service Ron Larson, U.S. Fish and Wildlife Service James Lecky, National Marine Fisheries Service Steven Lewis, U.S. Fish and Wildlife Service Loren Little, Modoc Irrigation District Douglas Markle, Oregon State University Graham Matthews, Graham Matthews & Associates Martin Miller, U.S. Fish and Wildlife Service Ken Maurer, Scott Valley resident David Mauser, U.S. Fish and Wildlife Service Frank McCormick, U.S. Forest Service Chris Mobley, National Marine Fisheries Service Curt Mullis, U.S. Fish and Wildlife Service Joseph Nelson, University of Alberta Roger Nicholson, Fort Klamath Rancher Todd Olson, PacifiCorp Felice Pace, Klamath Forest Alliance Ronnie Pierce, Karuk Tribe Richard Raymond, E&S Environmental Chemistry Inc.

Donald Reck, National Marine Fisheries Service Michael Rode, California Department of Fish and Game Kimball Rushton, Iron Gate Hatchery Michael Ryan, U.S. Bureau of Reclamation Ken Rykbost, Oregon State University Klamath Experiment Station David Sabo, U.S. Bureau of Reclamation Gary Scoppettone, U.S. Geological Survey Tom Shaw, U.S. Fish and Wildlife Service Rip Shively, U.S. Geological Survey Daniel Snyder, U.S. Geological Survey David Solem, Klamath Irrigation District Sari Sommarstrom, Consultant and President, California Watershed

Management Council

Endangered and Threatened Fishes in the Klamath River Basin: Causes of Decline and Strategies for ...

ACKNOWLEDGMENTS xi

Glen Spain, Pacific Coast Federation of Fisherman’s Associations, Institute for Fisheries Resources

Marshall Staunton, Upper Klamath Basin Working Group Mark Stern, The Nature Conservancy Ronald Sutton, U.S. Bureau of Reclamation Doug Tedrick, U.S. Bureau of Indian Affairs Larry Todd, U.S. Bureau of Reclamation Greg Tranah, Harvard School of Public Health Manuel Ulibarri, Dexter National Fish Hatchery and Technology Center Carl Ullman, Klamath Tribes David Vogel, Natural Resource Scientists, Inc.

Nancy Vucinich, Pyramid Lake Fisheries David Walters, U.S. Environmental Protection Agency Wedge Watkins, U.S. Bureau of Land Management David Webb, Shasta Coordinated Resources Management and Planning Faye Weekley, U.S. Fish and Wildlife Service Thomas Weimer, U.S. Department of the Interior Sam Williamson, U.S. Geological Survey Sue Ellen Wooldridge, U.S. Department of the Interior

The committee’s work also benefited from written and oral testimony submitted by the public, whose participation is much appreciated.

Endangered and Threatened Fishes in the Klamath River Basin: Causes of Decline and Strategies for ...

Endangered and Threatened Fishes in the Klamath River Basin: Causes of Decline and Strategies for ...

xiii

This report has been reviewed in draft form by persons chosen for their diverse perspectives and technical expertise in accordance with procedures approved by the National Research Council Report Review Committee. The purpose of this independent review is to provide candid and critical com-ments that will assist the institution in making its published report as sound as possible 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. The committee and the NRC thank the follow-ing for their review of this report:

Don Chapman, consultant, McCall, Idaho Jeff Curtis, Trout Unlimited Kurt Fausch, Colorado State University Wilford Gardner, University of California, Berkeley Stanley Gregory, Oregon State University Roger Kasperson, Stockholm Environment Institute James Kitchell, University of Wisconsin Mark Stern, The Nature Conservancy David Vogel, Natural Resource Scientists, Inc.

Robert Wetzel, University of North Carolina, Chapel Hill M. Gordon Wolman, Johns Hopkins University

Although the reviewers listed above have provided many constructive comments and suggestions, they were not asked to endorse the conclusions

Acknowledgment of Review Participants

Endangered and Threatened Fishes in the Klamath River Basin: Causes of Decline and Strategies for ...

xiv ACKNOWLEDGMENT OF REVIEW PARTICIPANTS or recommendations, nor did they see the final draft of the report before its release. The review of this report was overseen by Paul Risser, Oregon State University, and Stephen Berry, University of Chicago. Appointed by the Na-tional Research Council, 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 con-sidered. Responsibility for the final content of this report rests entirely with the committee and the National Research Council.

Endangered and Threatened Fishes in the Klamath River Basin: Causes of Decline and Strategies for ...

xv

The federal Endangered Species Act (ESA) of the United States has the admirable goal of minimizing extinction rates through regulations and ac-tions that are intended to produce recovery of species that are in critical decline. For any given species listed under the act, agencies implementing the ESA must choose from an immense array of possibilities the ones most likely to lead to recovery, and in doing so they must forego the luxury of an extended interval of monitoring or experimentation.

Remedies for the recovery of species often have harmful or at least frus-trating effects on people and institutions. In such instances, the affected parties often are especially dissatisfied with the implementation of remedies that are not absolutely secure scientifically. But the ESA does not allow delay, which would defeat its purpose. Thus, some of the remedies pre-scribed by agencies ultimately will prove ineffective and may cause eco-nomic or social disruption without any tangible benefit to listed species.

The National Research Council’s Committee on Endangered and Threatened Fishes in the Klamath River Basin deals in its final report with three Klamath basin fish species listed under the federal ESA. The com-mittee’s work is broad in that it encompasses the entire actual or potential range of those species in the Klamath basin, regardless of the boundaries set by ownership or management, and with all the potential environmental changes that could suppress or promote the welfare of the species. The com-mittee, in response to its charge, has given particular attention to evaluation of the certainty underlying specific kinds of remedies that might lead to the recovery of species. The issues that the committee has dealt with are specific

Preface

Endangered and Threatened Fishes in the Klamath River Basin: Causes of Decline and Strategies for ...

xvi PREFACE to the basin, but the Klamath basin presents in microcosm most of the prob-lems that are generally identified with implementation of the ESA. Espe-cially prominent in the Klamath basin is controversy over the extent to which remedies that have uncertain outcomes should be pursued even though they are economically or socially painful.

One issue especially well highlighted by the Klamath basin is the rela-tive weight that should be given to professional judgment as opposed to direct empirical evidence that appears to be contradictory to that judgment.

Whereas professional judgment is essential for successful ESA implementa-tions where site-specific information is absent, its use is more problematic when initial judgments fail empirical tests. Reversal of an initial judgment may seem to be an abandonment of duty or principle, but it is unrealistic to expect that all initial judgments will be proved scientifically sound. By rais-ing this issue in specific terms in its interim report, the committee has gener-ated considerable controversy in the Klamath basin. The committee believes, however, that a rational and consistent resolution of the issue works toward the long-term stability and effectiveness of the ESA. The committee’s final report gives a more detailed view of the committee’s approach.

The committee owes a great debt of gratitude to the National Research Council staff members who have guided it through the production of the final report. Suzanne van Drunick, project director, has been especially criti-cal to the success of the committee; David Policansky, James Reisa, and Bryan Shipley also helped the committee in numerous ways; Norman Grossblatt, Mirsada Karalic-Loncarevic, and Kelly Clark helped with the many details that made the report ready for publication. The committee is also appreciative of James MacMahon and other board members for their oversight of this study. The committee is grateful to Leslie Northcott of the University of Colorado for helping to produce the manuscript of the report and to Marylee Murphy and Rebecca Anthony of the University of Colo-rado for their work on figures and tables.

The committee benefited immensely from the help and advice of scien-tists and administrators who have dealt with environmental issues in the Klamath basin and to contributions from the citizens, organizations, and tribes working and living in the basin. The committee’s highest hope is that its work will be a contribution to the long-term general welfare of everyone who resides in, visits, or cares about the Klamath basin.

The National Research Council process for producing the report in-volves extensive reliance on external reviewers. The committee thanks the reviewers of its final report for their thoughtful contributions.

William M. Lewis, Jr., Chair Committee on Endangered and Threatened Fishes in the Klamath River Basin

Endangered and Threatened Fishes in the Klamath River Basin: Causes of Decline and Strategies for ...

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Contents

SUMMARY 1

1 INTRODUCTION 17

Overview of the Environment, 19 The Fishes, 26 Requirements of the Endangered Species Act, 28 Interested Parties, 30 The Committee, 33 Summary of the Biological Assessments and Biological Opinions of

2002, 37 Context for the Committee’s Report, 45

2 LAND USE AND WATER MANAGEMENT 46

Description of the Klamath River Watershed, 46 Aquatic Environments in the Upper Klamath Basin, 53 Aquatic Environments in the Lower Klamath Basin, 57 History of Land Use in the Klamath Basin, 57 Fishing and Attempts to Regulate Loss of Fish, 71 Wetland Transformations, 71 The Economy of the Klamath Basin, 74 Overview, 93

3 CURRENT STATUS OF AQUATIC ECOSYSTEMS: LAKES 95

Introduction, 95 Upper Klamath Lake, 97 Clear Lake, 129

Endangered and Threatened Fishes in the Klamath River Basin: Causes of Decline and Strategies for ...

xviii CONTENTS

Gerber Reservoir, 132 Lower Klamath Lake, 133 Tule Lake, 133 Reservoirs of the Main Stem, 134 Conclusions, 141

4 CURRENT AND HISTORICAL STATUS OF RIVER

AND STREAM ECOSYSTEM 144

Tributaries to Upper Klamath Lake (RM 337-270), 144 The Lost River, 146 The Main-Stem Klamath: Iron Gate Dam to Orleans

(RM 192-60), 147

The Shasta River (RM 177), 153 The Scott River (RM 143), 159 The Salmon River (RM 62), 168 The Trinity River (RM 43), 168 Minor Tributaries to the Lower Klamath Main Stem

(RM 192-0), 175

Main-Stem Klamath to the Pacific (RM 60-0), 176 Conclusions, 178

5 FISHES OF THE UPPER KLAMATH BASIN 179

Native Fishes, 180 Nonnative Fishes, 188 Endangered Suckers of the Klamath Basin, 189 Conclusions, 212

6 CAUSES OF DECLINE AND STRATEGIES FOR RECOVERY

OF KLAMATH BASIN SUCKERS 214

Criteria for Judging Status and Recovery of Sucker

Populations, 214 Requirements for Protection and Recovery, 217 Suppression of Endangered Suckers in Upper Klamath Lake, 219 Lessons from Comparative Biology of Suckers, 246 Conclusions, 247

7 FISHES OF THE LOWER KLAMATH BASIN 250

Coho Salmon, 252 Chinook Salmon, 263 Steelhead, 270 Other Fishes, 274 Mass Mortality of Fish in the Lower Klamath River in 2002, 278 Conclusions, 283

Endangered and Threatened Fishes in the Klamath River Basin: Causes of Decline and Strategies for ...

CONTENTS xix

8 FACILITATING RECOVERY OF COHO SALMON AND

OTHER ANADROMOUS FISHES OF THE

KLAMATH RIVER 287

Restoration of Tributaries, 287 The Main-Stem Klamath River, 298 The Lowermost Klamath and Ocean Conditions, 301 Removal of Dams, 302 Changes in Operation of Hatcheries, 303 Land-Management Practices, 304 Creation of a Framework for Fish Management, 305 Possible Future Effects of Climate Change, 307 Conclusions, 308

9 REGULATORY CONTEXT: THE ENDANGERED

SPECIES ACT 311

Overview of the ESA in the Klamath Context, 312 Species Listing and Designation of Critical Habitat, 316 Regulatory Consequences, 321 Conclusions, 329

10 ADAPTIVE MANAGEMENT FOR ECOSYSTEM

RESTORATION IN THE KLAMATH BASIN 331

Adaptive Management as an Organizing Framework, 332 Policy Options and Restoration Activities, 337 Improvement of Resource Management in the

Klamath Basin, 340 Conclusions, 343

11 RECOMMENDATIONS 344

Basinwide Issues, 344 Endangered Lost River and Shortnose Suckers, 346 Threatened Coho Salmon, 349 Costs, 352

REFERENCES 353

APPENDIX A Statement of Task 379

APPENDIX B Committee on Endangered and Threatened Fishes in the Klamath River Basin 381

INDEX 385

Endangered and Threatened Fishes in the Klamath River Basin: Causes of Decline and Strategies for ...

xx

BOX

S-1 Statement of Task, 4

FIGURES

S-1 Map of the Klamath River basin showing surface waters and landmarks, 2

1-1 Map of the upper Klamath River basin showing surface waters and landmarks mentioned in this report, 18

1-2 Water routing diagram for the Klamath Project, 21 1-3 Map of the upper Klamath basin, 23 1-4 Mainstem dams on the Klamath River, 24 1-5 Flow of the Williamson River, the largest water source for Upper

Klamath Lake, and of the Klamath River main stem (at Iron Gate Dam) in a year of near-average water availability, 26

2-1 General tectonic setting for northern California and southern Oregon illustrating the Cascadia subduction zone, the Cascade volcanic arc, the Basin and Range Province, and the Oregon fore-arc and Sierra Nevada blocks, 47

2-2 Changes in numbers of cattle and cumulative acres of drained wetland in Klamath County, Oregon, 64

2-3 Net loss, through drainage, of wetland connected to Upper Klamath Lake, 72

Box, Figures, and Tables

Endangered and Threatened Fishes in the Klamath River Basin: Causes of Decline and Strategies for ...

BOX, FIGURES, AND TABLES xxi

3-1 Bathymetric map of Upper Klamath Lake and Agency Lake showing depths at the mean summer lake elevation of 4,141 ft above sea level, 98

3-2 Water level of Upper Klamath Lake and mean water levels proposed by USBR for years of varying water availability, 100

3-3 Water level in Upper Klamath Lake in year of near-average mean water level (1999) and year of extremely low water level (lowest 5%; 1992), 101

3-4 Total phosphorus concentrations in Upper Klamath Lake during 1997 (an arbitrarily chosen year) and approximate discharge-weighted mean total phosphorus for inflow for background and for current conditions, 105

3-5 Change in chlorophyll a (lakewide averages, volume-weighted) over growing season for 2 consecutive years showing the potential interannual variability in development of chlorophyll maximums, 3-6 Relationship of mean chlorophyll (above) and peak chlorophyll (below) to water level in Upper Klamath Lake (median level for July and August), 113

3-7 Relationship between water level (median, July and August) and pH in Upper Klamath Lake, 115

3-8 Relationship between water level (median, July and August) and dissolved oxygen in the water column of Upper Klamath Lake, 120

3-9 Probable cause of low dissolved oxygen throughout the water column of Upper Klamath Lake during the growing season leading to mass mortality of fish, 121

3-10 Two contrasting hypotheses that may explain connections between human activity and high abundances of phytoplankton in Upper Klamath Lake, 124

3-11 Potential (?) and demonstrated (�) causal connections between high abundance of phytoplankton and harm to fish through poor water-quality conditions, 125

3-12 Map of Clear Lake, 130 3-13 Water temperature and dissolved oxygen (DO) in Copco and Iron

Gate Reservoirs, January 2000, 137 3-14 Water temperature and dissolved oxygen (DO) in all main-stem reservoirs, July 2000, 138 3-15 Longitudinal transect data on Keno Reservoir (Lake Ewauna), 13–

14 August 2001, 139

4-1 Relative external phosphorus loading from tributaries and other sources to Upper Klamath Lake, 145

Endangered and Threatened Fishes in the Klamath River Basin: Causes of Decline and Strategies for ...

xxii BOX, FIGURES, AND TABLES

4-2 Mean monthly flows at Iron Gate Dam in 1961–1996 compared with reconstructed flows for 1905–1912, 148

4-3 Simulated and measured temperature in the Klamath River below Iron Gate Dam, 149

4-4 Simulated daily maximum, mean, and minimum water temperatures on the Klamath River from Iron Gate Dam to Seiad Valley for Iron Gate Dam releases of 1,000 cfs (A) and 3,000 cfs (B) under meteorological conditions of August 14, 1996, 150

4-5 Mean annual concentrations of total nitrogen (TN) and total phosphorus (TP), nitrate (NO3

– expressed as N), and soluble reactive phosphorus (SRP) at two stations on the Klamath River, 152

4-6 Annual hydrograph for the lower Shasta River (at Yreka, California), from May 1999 to May 2001, 153

4-7 Map depicting substantial water diversions from the Shasta River below Dwinnell Dam, 155

4-8 Temperature (thin line) and daily average temperature (wide line) within the Shasta River below Dwinnell Dam during the summer of 2001, 158

4-9 Simulation of daily mean water temperatures in the Shasta River at three flows for August 2001 conditions, 159

4-10 Annual hydrograph of Scott River at Fort Jones, California, May 1999 through May 2001, 160

4-11 Declines in late summer and early fall flows on the Scott River, 164 4-12 Changes in cropping and water wells in the Scott Valley, 166 4-13 Plot of downstream changes in maximum weekly average water temperature on the main stem of the Scott River during summer, 167 4-14 Annual hydrograph of the Salmon River at Somes Bar, California, May 1999–May 2001, 169 4-15 Index map of the Trinity River watershed, 170 4-16 Example of regulated (dotted line, current recommended outflow) and unimpaired (solid line, inflow to Trinity Diversion Project) flows on the Upper Trinity River for water year 1973, a normal water year (40–60% exceedance probability for annual flow volume), 171

4-17 Average monthly discharge of the Klamath River at Klamath (USGS 11530500) and the Trinity River at Hoopa (USGS 11530000) for the period 1951–2002, 174

4-18 Water temperature (instantaneous daytime values) of the Klamath River at Orleans based on observations at USGS station 18010209, 1957–1980, plotted on a single annual time span, 177

5-1 Endangered suckers of the Klamath River basin, 190 5-2 Locations of current and past populations of Lost River suckers and shortnose suckers, 193

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BOX, FIGURES, AND TABLES xxiii

5-3 Generalized view of habitat of young suckers in Upper Klamath Lake, 197

5-4 Age distributions of suckers in Upper Klamath Lake based on fish kills, 205

5-5 Spawning-run abundances of lake suckers, lower Williamson River, 1995–2001, 206

5-6 Age structure of a small sample of shortnose suckers taken from Copco Reservoir, 1987, 210

6-1 Diagram of causal connections in suppression of populations of endangered suckers in Upper Klamath Lake, 221

6-2 Water levels for 5-day intervals in Upper Klamath Lake over months of most vigorous spawning by suckers (March, April, and May— MAM), shown in context with spawning habitat designations given by Reiser et al. (2001), 224

6-3 April water level and larval abundance (mean catch per unit effort [CPUE]) in Upper Klamath Lake, 225

6-4 Relative abundance of year classes of suckers in Upper Klamath Lake, as inferred from fish recovered after mass mortality in 1997, in relation to water level during spawning interval when same year classes were produced, 227

6-5 Relative abundance of larvae as determined by standardized sampling, shown in relation to mean water level of Upper Klamath Lake during the main interval of larval development (April–July), 6-6 Relative abundances of year classes of endangered suckers collected from Upper Klamath Lake during the fish kill of 1997, shown in relation to mean water level over the interval of larval development for the same year classes, 235

7-1 Coho salmon male (top), female (head), and parr, 254 7-2 Population cycles of coho salmon in California, 261 7-3 Mean flows of the Klamath main stem at Klamath (near the site of the 2002 fish kill) and at Iron Gate Dam (about 185 mi upstream) in September for 6 low-flow years considered by CDFG in its analysis of the fish kill, 280

TABLES

1-1 Flows Under Conditions of Average Water Availability in the Upper Klamath Basin, 22

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xxiv BOX, FIGURES, AND TABLES

1-2 Categories Used by the Committee for Judging the Degree of Scientific Support for Proposed Actions Pursuant to the Goals of the ESA, 35

1-3 Summary of Commitments of the USBR Biological Assessments of 2002 that are Relevant to the Two Endangered Sucker Species, 39

1-4 Summary of Components of USFWS Biological Opinions of 2002 that are Relevant to the Two Endangered Sucker Species of the Klamath River Basin, 40

1-5 Summary of Components of USBR Biological Assessments of 2002 that are Relevant to Threatened Coho Salmon of the Klamath River Basin, 42

1-6 Summary of Components of NMFS Biological Opinions of 2002 that are Relevant to Threatened Coho Salmon in the Klamath River Basin, 43

2-1 Runoff, Yield, and Basin Areas for the Klamath Watershed, 52 2-2 Structural Change in the Upper Klamath Basin Economy, 1969–1999, 75 2-3 Output, Value Added, and Employment in the Upper Klamath

Basin, 1998, 77 2-4 Export Based Employment, Upper Klamath Basin, 1998, 78 2-5 Characteristics of Upper Klamath Basin Farms and Farm Operators, 1997, 80 2-6 Value of Agricultural Production (Thousands of Dollars) in Upper

Klamath Basin, 1998, by County, 81 2-7 Farms in the Klamath Reclamation Project and in the Upper

Klamath Basin, 83 2-8 Structural Change in the Lower Klamath Basin Economy, 1969–1999, 85 2-9 Output, Value Added, and Employment in Lower Klamath Basin, 1998, 86 2-10 Export Based Employment, Lower Klamath Basin, 1998, 87 2-11 Characteristics of Lower Klamath Basin Farms and Farm Operators, 1997, 90 2-12 Value of Agricultural Production in the Lower Klamath Basin, 1998, 91 2-13 Fisheries Characteristics of Ports of Eureka (Humboldt County) and

Crescent City (Del Norte County), 92

3-1 Basic Information on Lakes of Upper Klamath Basin, 96 3-2 Status of Various Hypotheses Related to Water Quality of Upper

Klamath Lake, 123

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BOX, FIGURES, AND TABLES xxv

3-3 Summary of Grab-Sample Data for Surface Waters in the Main-Stem Reservoir System, 2001, 140

5-1 Native Fishes of the Upper Klamath Basin, 181 5-2 Nonnative Fishes of the Upper Klamath Basin, 189 5-3 Current and Former Distribution of Adult Lost River Suckers and

Shortnose Suckers in the Klamath Basin, 192

6-1 Summary of Status of Geographic Subpopulations of Two Endangered Suckers in Upper Klamath Basin, 216

6-2 Estimates of Larval Habitat Availability Calculated as Percentage of Lakeshore Inundated to a Depth of at Least 1 Ft for Lake Edge and Marsh Regions in Northeastern Upper Klamath Lake that Contain Emergent Vegetation, and Total Lake Shoreline Regardless of Vegetation, 233

6-3 Incidence (%) of Various Indicators of Stress in Suckers of Upper Klamath Lake Based on Visual Inspection, 239

7-1 Native Fishes of the Lower Klamath River and Its Tributaries, 251 7-2 Nonnative Fishes of the Lower Klamath and Trinity Rivers, 253 7-3 Pools Containing Juvenile Coho Salmon, Chinook Salmon, and

Steelhead Along Main Stem of Klamath River, 2001, as Determined in Snorkeling Surveys, 257

8-1 Factors Likely to Limit Production of Coho and Other Salmonids in the Shasta, Scott, Salmon, and Trinity Rivers and Their Tributaries, Endangered and Threatened Fishes in the Klamath River Basin: Causes of Decline and Strategies for ...

Endangered and Threatened Fishes in the Klamath River Basin: Causes of Decline and Strategies for ...

Summary

Two endemic fishes of the upper Klamath basin (Figure S-1), the short-nose sucker (Chasmistes brevirostris) and the Lost River sucker (Deltistes luxatus), were listed as endangered under the federal Endangered Species Act (ESA) in 1988 by the U.S. Fish and Wildlife Service (USFWS). USFWS cited overfishing, water management, habitat alteration, nonnative species, poor water quality, and several other factors as likely contributors to the decline of the fishes, which once were very abundant. In 1997, the Southern Oregon Northern California Coast “evolutionarily significant unit” of coho salmon (Oncorhynchus kisutch), which is native to the Klamath basin and several adjacent drainages, was listed by the National Marine Fisheries Service (NMFS) as threatened under the ESA. NMFS cited water manage-ment, water quality, loss of habitat, overfishing, and several other potential causes of decline for the coho salmon.

In 2001, in response to biological assessments prepared by the U.S.

Bureau of Reclamation (USBR), the two listing agencies issued biological opinions that required USBR to take numerous actions, including mainte-nance of higher water levels in Upper Klamath Lake and two reservoirs on the Lost River and higher flow of the Klamath River below Iron Gate Dam.

Release of the two biological opinions coincided with a severe drought.

Because of the new biological opinions and the drought, USBR was prohib-ited from releasing large amounts of water to farmers served by its Klamath Project, which diverts waters from Upper Klamath Lake and the upper Lost River for use in irrigation through USBR’s Klamath Project. The unex-pected restrictions on water supply, which severely impaired or eliminated

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2 FISHES IN THE KLAMATH RIVER BASIN

agricultural production on the 220,000 acres irrigated by the Klamath Project, caused agricultural water users and others to question the basis for water restrictions, while other parties, fearing adverse effects of the Klamath Project on the endangered and threatened fishes, supported the restrictions.

In late 2001, the Department of the Interior and the Department of Commerce asked the National Academies to form a committee (the Com-mittee on Endangered and Threatened Fishes in the Klamath River Basin)

Trinity Lake

Clear Lake

Tule Lake

Gerber Reservoir

Upper Klamath

Lake

Crater Lake

Lower Klamath Lake

Chiloquin

Falls Keno

C A L I F O R N I A

O R E G O N

Iron Gate Dam

Medford

Etna

Weaverville

Orleans

Lake Shastina

Dwinnell Dam

Klamath

FIGURE S-1 Map of the Klamath River basin showing surface waters and land-marks. Source: Modified from USFWS.

Endangered and Threatened Fishes in the Klamath River Basin: Causes of Decline and Strategies for ...

SUMMARY 3

to evaluate the strength of scientific support for the biological assessments and biological opinions on the three listed species, and to identify require-ments for recovery of the species. The committee was charged to complete an interim report in early 2002, focusing on effects of the Klamath Project, and to complete a final report in 2003 that would take a broad view of the scientific aspects of the continued survival of the listed species (Box S-1).

This is the committee’s final report.

In its interim report of February 2002, the committee found substantial scientific support for all recommendations made by the two listing agencies for the benefit of the endangered and threatened species, except for recom-mendations requiring more stringent controls over water levels in Upper Klamath Lake and flows at Iron Gate Dam. The committee also noted, however, that USBR had not provided any substantial scientific support for its own proposal of revised operating procedures, which might have led to lower mean water levels or lower minimum flows.

In 2002, USBR issued a new biological assessment that dealt with the two endangered sucker species and the threatened coho salmon. In re-sponse, USFWS prepared another biological opinion on the suckers, and NMFS prepared another biological opinion on the coho salmon. These documents reflect a closer interaction between the agencies than in previous years. USBR moved toward more restrictive operational practices than it had previously proposed and toward development of reserve water sup-plies; USFWS and NMFS were more cautious in requiring actions whose basis would be contradicted by site-specific studies, and they acknowledged the need to consult with parties in addition to USBR. The biological assess-ment and the two biological opinions for 2002 cover a 10-yr interval (2002– 2012), during which time the listing agencies may require additional con-sultation and may revise their biological opinions.

PRINCIPAL FINDINGS OF THE COMMITTEE

Lost River and Shortnose Suckers

Upper Klamath Lake

Although suckers of all age classes are present in Upper Klamath Lake, population densities of suckers are low, and there are no signs that the populations are returning to their previously high abundance.

Suckers spawn in tributaries to Upper Klamath Lake, but they are blocked from much potentially suitable spawning habitat by Chiloquin Dam on the Sprague River (Figure S-1). Numerous smaller blockages and diversions also are present but are poorly documented. Expansion of spawn-ing on the Sprague River could increase the abundance of fry descending to

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4 FISHES IN THE KLAMATH RIVER BASIN

Box S-1. Statement of Task

The committee will review the government’s biological opinions regarding the ef-fects of Klamath Project operations on species in the Klamath River Basin listed under the Endangered Species Act, including coho salmon and shortnose and Lost River suckers. The committee will assess whether the biological opinions are consistent with the available scientific information. It will consider hydrologic and other environmental parameters (including water quality and habitat availability) affecting those species at critical times in their life cycles, the probable conse-quences to them of not realizing those environmental parameters, and the inter-relationship of these environmental conditions necessary to recover and sustain the listed species.

To complete its charge, the committee will:

1. Review and evaluate the science underlying the Biological Assessments (USBR 2001a,b) and Biological Opinions (USFWS 2001; NMFS 2001).

2. Review and evaluate environmental parameters critical to the survival and recovery of listed species.

3. Identify scientific information relevant to evaluating the effects of project operations that has become available since USFWS and NMFS prepared the bio-logical opinions.

4. Identify gaps in the knowledge and scientific information that are needed to develop comprehensive strategies for recovering listed species and provide an estimate of the time and funding it would require.

A brief interim report will be provided by January 31, 2002. The interim report will focus on the February 2001 biological assessments of the Bureau of Reclama-tion and the April 2001 biological opinions of the U.S. Fish and Wildlife Service and National Marine Fisheries Service regarding the effects of operations of the Bu-reau of Reclamation’s Klamath Project on listed species. The committee will pro-vide a preliminary assessment of the scientific information used by the Bureau of Reclamation, the Fish and Wildlife Service, and the National Marine Fisheries Service, as cited in those documents, and will consider to what degree the analy-sis of effects in the biological opinions of the Fish and Wildlife Service and National Marine Fisheries Service is consistent with that scientific information. The commit-tee will identify any relevant scientific information it is aware of that has become available since the Fish and Wildlife Service and National Marine Fisheries Ser-vice prepared the biological opinions. The committee will also consider any other relevant scientific information of which it is aware.

The final report will thoroughly address the scientific aspects related to the continued survival of coho salmon and shortnose and Lost River suckers in the Klamath River Basin. The committee will identify gaps in the knowledge and scien-tific information that are needed and provide approximate estimates of the time and funding needed to fill those gaps, if such estimates are possible. The commit-tee will also provide an assessment of scientific considerations relevant to strate-gies for promoting the recovery of listed species in the Klamath Basin.

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SUMMARY 5

Upper Klamath Lake and would beneficially extend the interval over which they arrive at the lake.

The water quality of the tributaries to Upper Klamath Lake is poor for some native fishes but is probably adequate for the listed suckers. The tributaries do, however, show loss of riparian vegetation and wetland (largely due to agricultural practices), which could adversely influence the survival of fry. The physical condition of channels in general and spawning areas in particular is degraded, but the nature and extent of degradation is poorly documented for the tributaries.

Endangered suckers also spawn near springs that emerge at the margin of Upper Klamath Lake. Some apparently suitable spawning sites are no longer used, probably because entire groups of fish that used the sites were eliminated during the era of fishing, which ended in 1987. Lakeside spawn-ing behaviors are associated with a specific range of depth. During dry years, the amount of appropriate spawning substrate with appropriate wa-ter depth is reduced by drawdown of the lake. Data on year-class strength show no indication of a relationship between year-class strength and water level, which might be expected if drawdown were strongly suppressing pro-duction of fry.

Fry are strongly dispersed from their points of origin by currents and ultimately are found in shallow water in or near emergent vegetation at the margins of the lake. Loss of such vegetation, especially near the tributary mouths, could be disadvantageous to the fry. The area around the lake associated with preferred depths and presence of emergent vegetation varies with water level; drawdown, especially in dry years, reduces this area.

Standardized sampling of fry and studies of year-class strength for large fish do not, however, indicate associations between water level and abundance of larvae.

Juveniles seek somewhat…