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NDANGERED AND THREATENED FISHES I N TH E KLAMATH RIVER BASIN CAUSES OF DECLINE AND STRATEGIES FOR RECOVERY Committee on Enclangerecl and Threatenecl Fishes in the Klamath River Basin Boarcl on Environmental Stuclies ancl Toxicology Division on Earth and Life Stuclies NATIONAL RESEARCH COUNCIL OF THE NATIONAL ACADEMIES THE NATIONAL ACADEMIES PRESS Washington, DC www.nap.edu

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THE NATIONAL ACADEMIES PRESS 500 Fifth Street, N.W. 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 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 I(lamath River Basin: causes of decline and . strategies: -or recovery. p. cm. Includes bibliographical references (p. ). IS8N 0-309-09097-0 (hardcover) IS8N 0-309-52808-9 (pdf) 1. Rare fishes I(lamath River Watershed (Or. and Calif.) 2. Fishes Conserva- tion I(lamath 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. 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 Copyright 2004 by the National Academy of Sciences. All rights reserved. Printed in the United States of America.

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THE NATIONAL ACADEMIES Advisers to the Nation on Stiente, Engineering, and Meditine 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. Bruce M. Alberts 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 engi- neers. 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. Wm. A. Wulf is president of the National Academv of Engineering. The Institute of Medicine was established in 1970 by the National Academy of Sci- ences to secure the services of eminent members of appropriate professions in the examination of policy matters pertaining to the health of the public. The Institute acts under the responsibility given to the National Academy of Sciences by its con- gressional 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 Sciences 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 gov- ernment, the public, and the scientific and engineering communities. The Council is administered jointly by both Academies and the Institute of Medicine. Dr. Bruce M. Alberts and Dr. Wm. A. Wulf are chair and vice chair, respectively, of the National Research Council. www.national-academies.org

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COMMITTEE ON ENDANGERED AND THREATENED FISHES IN THE KLAMATH RIVER BASIN Members WILLIAM M. LEWIS, IR. (Chair), University of Coloraclo, Bouicler RICHARD M. ADAMS, Oregon State University, Corvallis ELLIS B. COWLING, North Carolina State University, Raleigh EUGENE S. HEEFMAN, University of Georgia, Athens CHARLES D. D. HOWARD, Consulting Engineer, Victoria, British Columbia, Canacia ROBERT I. 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 I. NEWCOMB, Michigan Department of Natural Resources, Lansing MICHAEL L. PACE, Institute of Ecosystem StucTies, Milibrook, NY }.B. RUHL, Floricia State University, Tallahassee Staff SUZANNE VAN DRUNICK, Project Director DAVID I. POLICANSKY, Associate Director anti Senior Program Director for AppliecI Ecology NORMAN GROSSBEATT, Senior Editor KELLY CLARK, Assistant Editor MIRSADA KARAETC-LONCAREVIC, Research Assistant BRYAN P. SHIPLEY, Research Assistant Sponsors U.S. DEPARTMENT OF THE INTERIOR U.S. DEPARTMENT OF COMMERCE v

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BOARD ON ENVIRONMENTAL STUDIES AND TOXICOLOGY1 Members JONATHAN M. SAMET (ChairJ, lohns Hopkins University, Baltimore, MD DAVID ALLEN, University of Texas, Austin THOMAS BURKE, IOhnS 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 anti Science University, Beaverton SHERRI W. GOODMAN, Center for Naval Analyses, AlexancTria, 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 StucTies, Milibrook, 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 TIEMAN, University of Minnesota, St. Paul CHRIS G. WHIPPLE, Environ Incorporated, Emeryville, CA LAUREN A. ZETSE, California Environmental Protection Agency, OaklancT, CA Senior Staff JAMES }. RETSA, Director DAVID I. POETCANSKY, Associate Director RAYMOND A. WASSEL, Senior Program Director for Environmental Sciences ancT Engineering KULBIR BAKSHT, Program Director for the Committee on Toxicology ROBERTA M. WEDGE, Program Director for Risk Analysis K. JOHN HOLMES, Senior Staff Officer SUSAN N. }. MARTEE, 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 iThis study was planned, overseen, and supported by the Board on Environmental Studies and Toxicology. v'

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OTHER REPORTS OF THE BOARD ON ENVIRONMENTAL STUDIES AND TOXICOLOGY Cumulative Environmental Effects of Alaska North Slope Oil ancI Gas Development (2003) Estimating the Public Health Benefits of Proposed Air Pollution Regulations (2002) Biosolicis AppliecI to LancI: Advancing Stanciarcis anti Practices (2002) Ecological Dynamics on Yellowstone's Northern Range (2002) The Airliner Cabin Environment ancI Health of Passengers ancI Crew (2002) Arsenic in Drinking Water: 2001 Update (2001 ~ Evaluating Vehicle Emissions Inspection ancI Maintenance Programs (2001 ~ Compensating for WetiancI Losses Uncler the Clean Water Act (2001) A Risk-Management Strategy for PCB-ContaminatecI Sediments (2001) Acute Exposure Guicleline Levels for SelectecI Airborne Chemicals (3 volumes; 2000-2003) Toxicological Effects of Methy~mercury (2000) Strengthening Science at the U.S. Environmental Protection Agency (2000) Scientific Frontiers in Developmental Toxicology ancI Risk Assessment (2000) Ecological Indicators for the Nation (2000) Mocleling Mobile-Source Emissions (2000) Waste Incineration ancI Public Health (1999) Hormonally Active Agents in the Environment (1999) Research Priorities for Airborne Particulate Matter (4 volumes, 1998-2003) Ozone-Forming Potential of ReformulatecI Gasoline (1999) Arsenic in Drinking Water ~ 1999) The National Research Council's Committee on Toxicology: The First 50 Years (1997) . ~ . Carcinogens ancI Anticarcinogens in the Human Diet (1996) Upstream: Salmon ancI Society in the Pacific Northwest (1996) Science anti the EnciangerecI Species Act (1995) Wetiancis: Characteristics ancI Boundaries (1995) Biologic Markers (5 volumes, 1989-1995 ~ Review of EPA's Environmental Monitoring anti Assessment Program (3 volumes, 1994-1995) Science anti lucigment in Risk Assessment (1994) Pesticides in the Diets of Infants anti Chilciren (1993) Dolphins anti the Tuna Industry (1992) . . v''

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Science anti the National Parks (1992) Human Exposure Assessment for Airborne Pollutants (1991) Rethinking the Ozone Problem in Urban anti 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 . . . v'''

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Acknowledgments This project was supported by the U.S. Bureau of Reclamation (USBR), the U.S. Fish ancI WilcIlife Service (USFWS), ancI the National Marine Fish- eries Service (NMFS). Many people assisted the committee ancI National Research Council staff in creating this report. We are grateful for the support proviclecI by the following: Pablo Arroyave, U.S. Bureau of Reclamation Ec~warcI Bartell, Water for Life Foundation lohn Bartholow, U.S. Geological Survey Michael Belchik, Yurok Tribe Antonio Bentivoglio, U.S. Fish ancI WilcIlife Service Gary Black, Siskiyou Resource Conservation District Rancly Brown, U.S. Fish ancI WilcIlife Service Mark Buettner, U.S. Fish ancI WilcIlife Service DonalcI Buth, University of California, Los Angeles lames Carpenter, Carpenter Design Inc. William Chesney, California Department of Fish ancI Game Paul Cleary, Oregon Department of Water Resources David Cottingham, Marine Mammal Commission lohn Crawford, Tule Lake Irrigation District Ear! Danosky, Tule Lake Irrigation District Michael Deas, Watercourse Engineering Inc. Thomas Dowling, Arizona State University Larry Dunsmoor, I(lamath Tribes Natural Resources 1 -

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x lohn Fay, U.S. Fish ancI WilcIlife Service Mary Freeman, U.S. Geological Survey Thomas Harcly, Utah Water Research Laboratory William Hogarth, National Marine Fisheries Service Becky Hycle, Yainex Ranch Owner Cecil lennings, U.S. Geological Survey Marshall [ones, U.S. Fish ancI WilcIlife Service lohn I(eys, III, U.S. Bureau of Reclamation lacob I(ann, Aquatic Ecosystem Sciences LLC Steve Kirk, Oregon Department of Environmental Quality Don I(nowles, National Marine Fisheries Service Ron Larson, U.S. Fish ancI WilcIlife Service Tames Lecky, National Marine Fisheries Service Steven Lewis, U.S. Fish ancI WilcIlife Service Loren Little, Mocloc Irrigation District Douglas Markle, Oregon State University Graham Matthews, Graham Matthews & Associates Martin Miller, U.S. Fish ancI WilcIlife Service I(en Maurer, Scott Valley resident DavicI Mauser, U.S. Fish ancI WilcIlife Service Frank McCormick, U.S. Forest Service Chris Mobley, National Marine Fisheries Service Curt Mullis, U.S. Fish ancI WilcIlife Service loseph Nelson, University of Alberta Roger Nicholson, Fort I(lamath Rancher TocicI Olson, PacifiCorp Felice Pace, I(lamath Forest Alliance Ronnie Pierce, I(aruk Tribe RicharcI RaymoncI, E&S Environmental Chemistry Inc. DonalcI Reck, National Marine Fisheries Service Michae! Rocle, California Department of Fish ancI Game I(imball Rushton, Iron Gate Hatchery Michae! Ryan, U.S. Bureau of Reclamation I(en Rykbost, Oregon State University I(lamath Experiment Station DavicI Sabo, U.S. Bureau of Reclamation Gary Scoppettone, U.S. Geological Survey Tom Shaw, U.S. Fish ancI WilcIlife Service Rip Shively, U.S. Geological Survey Danie! Snycler, U.S. Geological Survey DavicI Solem, I(lamath Irrigation District Sari Sommarstrom, Consultant ancI Presiclent, California WatershecI Management Council ACKNO WLEDGMENTS

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ACKNO WLEDGMENTS X1 Glen Spain, Pacific Coast Federation of Fisherman's Associations, Institute for Fisheries Resources Marshall Staunton, Upper I(lamath Basin Working Group Mark Stern, The Nature Conservancy RonalcI Sutton, U.S. Bureau of Reclamation Doug Tecirick, U.S. Bureau of Indian Affairs Larry TocicI, U.S. Bureau of Reclamation Greg Tranah, Harvard School of Public Health Manuel Ulibarri, Dexter National Fish Hatchery anti Technology Center Car! Uliman, I(lamath Tribes David Vogel, Natural Resource Scientists, Inc. Nancy Vucinich, Pyramid Lake Fisheries David Walters, U.S. Environmental Protection Agency Wecige Watkins, U.S. Bureau of LancI Management David Webb, Shasta CoorclinatecI Resources Management anti Planning Faye Weekley, U.S. Fish anti WilcIlife Service Thomas Weimer, U.S. Department of the Interior Sam Williamson, U.S. Geological Survey Sue Ellen Wooiciricige, U.S. Department of the Interior The committee's work also benefited from written ancT oral testimony submitted by the public, whose participation is much appreciated.

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xv! PREFACE to the basin, but the I(lamath basin presents in microcosm most of the prob- lems that are generally iclentifiecI with implementation of the ESA. Espe- cially prominent in the I(lamath basin is controversy over the extent to which remedies that have uncertain outcomes shouicI be pursued even though they are economically or socially painful. One issue especially well highlightecI by the I(lamath basin is the rela- tive weight that shouicI be given to professional judgment as opposed to clirect 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 cluty or principle, but it is unrealistic to expect that all initial judgments will be provecI scientifically souncI. By rais- ing this issue in specific terms in its interim report, the committee has gener- atecI consiclerable controversy in the I(lamath basin. The committee believes, however, that a rational anti consistent resolution of the issue works toward the long-term stability anti effectiveness of the ESA. The committee's final report gives a more cletailecI view of the committee's approach. The committee owes a great clebt of gratitude to the National Research Council staff members who have guiclecI it through the production of the final report. Suzanne van Drunick, project director, has been especially criti- cal to the success of the committee; DavicI Policansky, lames Reisa, anti Bryan Shipley also helpecI the committee in numerous ways; Norman Grossblatt, Mirsacia I(aralic-Loncarevic, anti I(elly Clark helpecI with the many cletails that macle the report reacly for publication. The committee is also appreciative of lames MacMahon anti other boarcI members for their oversight of this study. The committee is grateful to Leslie Northcott of the University of Coloraclo for helping to produce the manuscript of the report anti to Marylee Murphy anti Rebecca Anthony of the University of Colo- raclo for their work on figures anti tables. The committee benefited immensely from the help anti advice of scien- tists anti administrators who have clealt with environmental issues in the I(lamath basin anti to contributions from the citizens, organizations, anti tribes working anti 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 resicles in, visits, or cares about the I(lamath 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, tr., Chair Committee on EnciangerecI anti Threatened Fishes in the I(lamath River Basin

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Contents SUMMARY 1 INTRODUCTION Overview of the Environment, 19 The Fishes, 26 Requirements of the EnciangerecI Species Act, 28 Interested Parties, 30 The Committee, 33 Summary of the Biological Assessments anti Biological Opinions of 2002, 37 Context for the Committee's Report, 45 2 LAND USE AND WATER MANAGEMENT Description of the I(lamath River Watershed, 46 Aquatic Environments in the Upper I(lamath Basin, 53 Aquatic Environments in the Lower I(lamath Basin, 57 History of LancI Use in the I(lamath Basin, 57 Fishing anti Attempts to Regulate Loss of Fish, 71 WetiancI Transformations, 71 The Economy of the I(lamath Basin, 74 Overview, 93 1 17 46 CURRENT STATUS OF AQUATIC ECOSYSTEMS: LAI(ES 95 Introduction, 95 Upper I(lamath Lake, 97 Clear Lake, 129 . . xv''

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. . . xvIll Gerber Reservoir, 132 Lower I(lamath Lake, 133 Tule Lake, 133 Reservoirs of the Main Stem, 134 Conclusions, 141 4 CURRENT AND HISTORICAL STATUS OF RIVER AND STREAM ECOSYSTEM Tributaries to Upper I(lamath Lake (RM 337-270), 144 The Lost River, 146 The Main-Stem I(lamath: Iron Gate Dam to Orieans (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 I(lamath Main Stem (RM 192-0), 175 Main-Stem I(lamath to the Pacific (RM 60-0), 176 Conclusions, 178 FISHES OF THE UPPER I(LAMATH BASIN Native Fishes, 180 Nonnative Fishes, 188 EnciangerecI Suckers of the I(lamath Basin, 189 Conclusions, 212 CAUSES OF DECLINE AND STRATEGIES FOR RECOVERY OF I(LAMATH BASIN SUCI(ERS Criteria for luciging Status ancT Recovery of Sucker Populations, 214 Requirements for Protection ancT Recovery, 217 Suppression of EnciangerecT Suckers in Upper I(lamath Lake, 219 Lessons from Comparative Biology of Suckers, 246 Conclusions, 247 FISHES OF THE LOWER I(LAMATH BASIN Coho Salmon, 252 Chinook Salmon, 263 SteelheacT, 270 Other Fishes, 274 Mass Mortality of Fish in the Lower I(lamath River in 2002, 278 Conclusions, 283 CONTENTS 144 179 214 250

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CONTENTS 8 FACILITATING RECOVERY OF COHO SALMON AND OTHER ANADROMOUS FISHES OF THE I(LAMATH RIVER Restoration of Tributaries, 287 The Main-Stem I(lamath River, 298 The Lowermost I(lamath anti Ocean Conditions, 301 Removal of Dams, 302 Changes in Operation of Hatcheries, 303 LancI-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 Overview of the ESA in the I(lamath Context, 312 Species Listing anti Designation of Critical Habitat, 316 Regulatory Consequences, 321 Conclusions, 329 10 ADAPTIVE MANAGEMENT FOR ECOSYSTEM RESTORATION IN THE I(LAMATH BASIN Adaptive Management as an Organizing Framework, 332 Policy Options anti Restoration Activities, 337 Improvement of Resource Management in the I(lamath Basin, 340 Conclusions, 343 11 RECOMMENDATIONS Basinwicle Issues, 344 EnciangerecT Lost River ancT Shortnose Suckers, 346 Threatened Coho Salmon, 349 Costs, 352 REFERENCES APPENDIX A Statement of Task APPEND IX B Committee on En ciangere cI an cI Threatene cI Fishes in the I(lamath River Basin INDEX X1 - 287 311 331 344 353 379 381 385

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Box, Figures, and Tables BOX S-1 Statement of Task, 4 FIGURES S-1 Map of the I(lamath River basin showing surface waters anti lancimarks, 2 1-1 Map of the upper I(lamath River basin showing surface waters anti lancimarks mentioned in this report, 18 Water routing diagram for the I(lamath Project, 21 Map of the upper I(lamath basin, 23 Mainstem clams on the I(lamath River, 24 Flow of the Williamson River, the largest water source for Upper I(lamath Lake, anti of the I(lamath River main stem (at Iron Gate Dam) in a year of near-average water availability, 26 General tectonic setting for northern California anti southern Oregon illustrating the Cascaclia subduction zone, the Cascade volcanic arc, the Basin anti Range Province, anti the Oregon fore-arc anti Sierra Nevada blocks, 47 Changes in numbers of cattle anti cumulative acres of cirainecI wetiancI in I(lamath County, Oregon, 64 2-3 Net loss, through drainage, of wetiancI connected to Upper I(lamath Lake, 72 xx

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B OX, FIG URES, AND TABLES X~1 Bathymetric map of Upper I(lamath Lake ancI Agency Lake showing depths at the mean summer lake elevation of 4,141 ft above sea level, 98 Water level of Upper I(lamath Lake ancI mean water levels proposed by USER for years of varying water availability, 100 Water level in Upper I(lamath Lake in year of near-average mean water level (1999) ancI year of extremely low water level (lowest 5/O; 1992), 101 Total phosphorus concentrations in Upper I(lamath Lake cluring 1997 (an arbitrarily chosen year) ancI approximate clischarge- weightecI mean total phosphorus for inflow for background anti for current conditions, 105 3-5 Change in chlorophyll a (lakewicle averages, volume-weightecI) over growing season for 2 consecutive years showing the potential interannual variability in clevelopment of chlorophyll maximums, 111 Relationship of mean chlorophyll (above) ancI peak chlorophyll (below) to water level in Upper I(lamath Lake (meclian level for luly ancI August), 113 Relationship between water level (meclian, luly ancI August) ancI pH in Upper I(lamath Lake, 115 Relationship between water level (meclian, luly ancI August) anti clissolvecI oxygen in the water column of Upper I(lamath Lake, 120 Probable cause of low clissolvecI oxygen throughout the water column of Upper I(lamath Lake cluring the growing season leacling to mass mortality of fish, 121 3-10 Two contrasting hypotheses that may explain connections between human activity anti high abundances of phytoplankton in Upper I(lamath Lake, 124 3-11 Potential (?) anti clemonstratecI (,/) causal connections between high abundance of phytoplankton anti harm to fish through poor water- quality conditions, 125 3-12 Map of Clear Lake, 130 3-13 Water temperature anti clissolvecI oxygen (DO) in Copco anti Iron Gate Reservoirs, lanuary 2000, 137 3-14 Water temperature anti clissolvecI oxygen (DO) in all main-stem reservoirs, luly 2000, 138 3-15 Longituclinal transect ciata on I(eno Reservoir (Lake Ewauna), 13- 14 August 2001, 139 4-1 Relative external phosphorus loacling from tributaries anti other sources to Upper I(lamath Lake, 145 3-6 3-7 3-8

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. . X- 11 B OX, FIG URES, AND TABLES Mean monthly flows at Iron Gate Dam in 1961-1996 compared with reconstructed flows for 1905-1912' 148 4-3 SimulatecI ancI measured temperature in the I(lamath River below Iron Gate Dam, 149 4-4 SimulatecI ciaily maximum, mean, ancI minimum water temperatures on the I(lamath River from Iron Gate Dam to SeiacI Valley for Iron Gate Dam releases of 1,000 cfs (A) ancI 3~000 cfs (B) uncler meteorologicalconclitionsof august 14,1996,150 4-5 Mean annual concentrations of total nitrogen (TN) ancI total phosphorus (TP), nitrate (NO3-expressecI as N), ancI soluble reactive phosphorus (SRP) at two stations on the I(lamath River, 152 4-6 Annual hycirograph 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) ancI ciaily average temperature (wicle line) within the Shasta River below Dwinnell Dam cluring the summer of 2001' 158 4-9 Simulation of ciaily mean water temperatures in the Shasta River at three flows for August 2001 conditions, 159 4-10 Annual hycirograph of Scott River at Fort [ones, California, May 1 999 through May 2001' 160 4-11 Declines in late summer ancI early fall flows on the Scott River, 164 4-12 Changes in cropping ancI 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 cluring summer, 167 4-14 Annual hycirograph of the Salmon River at Somes Bar, California, May 1 999-May 2001 ~ 169 4-15 Inclex map of the Trinity River watershed, 170 4-16 Example of regulatecI (clottecI line, current recommenclecI outflow) ancI unimpaired (solicI line, inflow to Trinity Diversion Project) flows on the Upper Trinity River for water year 1973' a normal water year (40-60% exceeciance probability for annual flow volume), 171 4-17 Average monthly discharge of the I(lamath River at I(lamath (USGS 11530500) and the Trinity River at Hoopa (USGS 11530000) for the period 1 95 1-2002' 1 74 4-18 Water temperature (instantaneous daytime values) of the I(lamath River at Orieans basecI on observations at USGS station 18010209' 1957-1980' plottecI on a single annual time span, 177 EnciangerecI suckers of the I(lamath River basin, 190 Locations of current ancI past populations of Lost River suckers ancI shortnose suckers, 193

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B OX, FIG URES, AND TABLES 5-4 5-5 X- 111 5-3 GeneralizecI view of habitat of young suckers in Upper I(lamath Lake, 197 Age distributions of suckers in Upper I(lamath Lake basecI on fish kills, 205 Spawning-run abundances of lake suckers, lower Williamson River, 1995-2001,206 Age structure of a small sample of shortnose suckers taken from Copco Reservoir, 1987,210 Diagram of causal connections in suppression of populations of enciangerecI suckers in Upper I(lamath Lake, 221 Water levels for 5-clay intervals in Upper I(lamath Lake over months of most vigorous spawning by suckers (March, April, anti May- MAM), shown in context with spawning habitat designations given by Reiser et al. (2001),224 April water level anti larval abundance (mean catch per unit effort LCPUE] ~ in Upper I(lamath Lake, 225 Relative abundance of year classes of suckers in Upper I(lamath Lake, as inferred from fish recovered after mass mortality in 1997, in relation to water level cluring spawning interval when same year classes were proclucecI, 227 6-5 Relative abundance of larvae as cleterminecI by stanciarclizecI sampling, shown in relation to mean water level of Upper I(lamath Lake cluring the main interval of larval clevelopment (April-luly), 235 6-6 Relative abundances of year classes of enciangerecI suckers collectecI from Upper I(lamath Lake cluring the fish kill of 1997, shown in relation to mean water level over the interval of larval clevelopment for the same year classes, 235 7-1 Coho salmon male (top), female (heacI), anti Parr, 254 7-2 Population cycles of coho salmon in California, 261 Mean flows of the I(lamath main stem at I(lamath (near the site of the 2002 fish kill) anti at Iron Gate Dam (about 185 mi upstream) in September for 6 low-flow years consiclerecI by CDFG in its analysis of the fish kill, 280 TABLES 1-1 Flows Uncler Conditions of Average Water Availability in the Upper I(lamath Basin, 22

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xxiv 1-3 1-4 B OX, FIG URES, AND TABLES 1-2 Categories Used by the Committee for fudging the Degree of Scientific Support for Proposed Actions Pursuant to the Goals of the ESA, 35 Summary of Commitments of the USER Biological Assessments of 2002 that are Relevant to the Two Endangered Sucker Species, 39 Summary of Components of USFWS Biological Opinions of 2002 that are Relevant to the Two Endangered Sucker Species of the I(lamath River Basin, 40 Summary of Components of USER Biological Assessments of 2002 that are Relevant to Threatened Coho Salmon of the I(lamath River Basin, 42 1-6 Summary of Components of NMFS Biological Opinions of 2002 that are Relevant to Threatened Coho Salmon in the I(lamath River Basin, 43 2-3 2-5 2-1 Runoff, Yield, and Basin Areas for the I(lamath Watershed, 52 Structural Change in the Upper I(lamath Basin Economy, 1969-1999, 75 Output, Value Added, and Employment in the Upper I(lamath Basin, 1998, 77 2-4 Export Based Employment, Upper I(lamath Basin, 1998, 78 Characteristics of Upper I(lamath Basin Farms and Farm Operators, 1997, 80 2-6 Value of Agricultural Production (Thousands of Dollars) in Upper I(lamath Basin, 1998, by County, 81 Farms in the I(lamath Reclamation Project and in the Upper I(lamath Basin, 83 2-8 Structural Change in the Lower I(lamath Basin Economy, 1969-1999, 85 2-9 Output, Value Added, and Employment in Lower I(lamath Basin, 1998, 86 2-10 Export Based Employment, Lower I(lamath Basin, 1998, 87 2-11 Characteristics of Lower I(lamath Basin Farms and Farm Operators' 1997, 90 2-12 Value of Agricultural Production in the Lower I(lamath Basin, 1998, 91 2-13 Fisheries Characteristics of Ports of Eureka (Humboldt County) and Crescent City (Del Norte County), 92 Basic Information on Lakes of Upper I(lamath Basin, 96 Status of Various Hypotheses Related to Water Quality of Upper I(lamath Lake, 123

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B OX, FIG URES, AND TABLES XXV Summary of Grab-Sample Data for Surface Waters in the Main-Stem Reservoir System, 2001, 140 5-1 5-2 5-3 Native Fishes of the Upper I(lamath Basin, 181 Nonnative Fishes of the Upper I(lamath Basin, 189 Current anti Former Distribution of Aclult Lost River Suckers anti Shortnose Suckers in the I(lamath Basin, 192 Summary of Status of Geographic Subpopulations of Two EnciangerecI Suckers in Upper I(lamath Basin, 216 Estimates of Larval Habitat Availability CalculatecI as Percentage of Lakeshore InunciatecI to a Depth of at Least 1 Ft for Lake Ecige anti Marsh Regions in Northeastern Upper I(lamath Lake that Contain Emergent Vegetation, anti Total Lake Shoreline RegarcIless of Vegetation, 233 Incidence (/O) of Various Indicators of Stress in Suckers of Upper I(lamath Lake Based on Visual Inspection, 239 Native Fishes of the Lower I(lamath River ancT Its Tributaries, 251 Nonnative Fishes of the Lower I(lamath ancT Trinity Rivers, 253 Pools Containing luvenile Coho Salmon, Chinook Salmon, ancT SteelheacT Along Main Stem of I(lamath River, 2001, as Determined in Snorkeling Surveys, 257 Factors Likely to Limit Production of Coho ancT Other SalmonicTs in the Shasta, Scott, Salmon, ancT Trinity Rivers ancT Their Tributaries, 288

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