A Scientific Assessment of Alternatives for Reducing Water Management Effects on Threatened and Endangered Fishes in California’s Bay–Delta

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A Scientific Assessment of Alternatives for Reducing Water Management Effects on Threatened and Endangered Fishes in California’s Bay–Delta Committee on Sustainable Water and Environmental Management in the California Bay-Delta Water Science and Technology Board Ocean Studies Board Division on Earth and Life Studies THE NATIONAL ACADEMIES PRESS Washington, D.C. www.nap.edu

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THE NATIONAL ACADEMIES PRESS 500 Fifth Street, N.W. Washington, D.C. 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 panel responsible for the report were chosen for their special competences and with regard for appropriate balance. Support for this study was provided by the Department of the Interior under contract no. 80221-A-G100. Any opinions, findings, conclusions, or recommendations ex- pressed in this publication are those of the author(s) and do not necessarily reflect the views of the organizations or agencies that provided support for the project. International Standard Book Number-13: 978-0-309-12802-5 International Standard Book Number-10: 0-309-12802-1 Additional copies of this report are available from the National Academies Press, 500 5th Street, N.W., Lockbox 285, Washington, D.C. 20055; (800) 624-6242 or (202) 334-3313 (in the Washington metropolitan area); Internet, http://www.nap.edu. Photo of the California Bay-Delta on the cover is courtesy of David Policansky. Cover was designed by Sharon Martin. Copyright 2010 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 Academy 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 engineers. 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 engineering programs aimed at meeting national needs, encourages education and research, and recognizes the superior achievements of engineers. Dr. Charles M. Vest is president 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 Institute acts under the re- sponsibility 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 Insti- tute 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 Na- tional Academy of Engineering in providing services to the government, the public, and the scientific and engineering communities. The Council 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 SUSTAINABLE WATER AND ENVIRONMENTAL MANAGEMENT IN THE CALIFORNIA BAY-DELTA* ROBERT J. HUGGETT, Chair, Professor Emeritus, College of William and Mary, Seaford, Virginia JAMES J. ANDERSON, University of Washington, Seattle MICHAEL E. CAMPANA, Oregon State University, Corvallis THOMAS DUNNE, University of California, Santa Barbara ALBERT E. GIORGI, BioAnalysts, Inc., Redmond, Washington PATRICIA M. GLIBERT, University of Maryland Center for Environmental Science, Horn Point Laboratory, Cambridge CHRISTINE A. KLEIN, University of Florida College of Law, Gainesville SAMUEL N. LUOMA, John Muir Institute of the Environment, University of California, Davis MICHAEL J. MCGUIRE, Michael J. McGuire, Inc., Santa Monica, California THOMAS MILLER, University of Maryland Center for Environmental Science, Chesapeake Biological Laboratory, Solomons, Maryland JAYANTHA OBEYSEKERA, South Florida Water Management District, West Palm Beach MAX J. PFEFFER, Cornell University, Ithaca, New York DENISE J. REED, University of New Orleans, New Orleans, Louisiana KENNETH A. ROSE, Louisiana State University, Baton Rouge DESIREE D. TULLOS, Oregon State University, Corvallis NRC Staff DAVID POLICANSKY, NRC Study Director, Scholar LAURA J. HELSABECK, Deputy Study Director STEPHEN D. PARKER, WSTB Director, Scholar SUSAN ROBERTS, OSB Director ELLEN A. DE GUZMAN, Research Associate HEATHER CHIARELLO, Senior Program Assistant * Biographical information for committee members is in Appendix E. This project was organized and overseen by the NRC’s Water Science and Technology Board (lead) and Ocean Studies Board, whose rosters are in Appendixes B and C, respectively. v

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Preface California, like many states, faces challenges related to water. Much of the state is too dry to support many human activities, such as municipal and indus- trial water use and irrigated agriculture, without supplementing the natural water supply. It has done this through an extensive series of engineering projects that include reservoirs, canals, levees, and pumps, largely to move water from the more humid north to the more arid and densely populated south. Much of Cali- fornia’s natural surface-water supply flows into and through the Sacramento and San Joaquin watersheds into California’s Bay-Delta, and from there through San Francisco Bay into the ocean. The delta itself is a biologically diverse estuarine ecosystem, and is the main point of diversion for water that is transported to the south. As California’s population and economic activity have increased, along with water diversions from the delta, conflicts over various water uses have in- creased as well, especially surrounding the bay-delta. Those conflicts have been brought to a head by restrictions on water diversions that have been required by two biological opinions, one by the U.S. Fish and Wildlife Service, covering delta smelt, and one by the National Marine Fisheries Service, covering salmon, steelhead, and sturgeon, to protect those fishes, which are listed as threatened or endangered under the federal Endangered Species Act. In addition, several re- cent dry years have exacerbated the situation. Conflicts over water are not new in California, but the current conflicts over the bay-delta appear to be unprece- dented in their scale. Few parts of the state are unaffected by what happens to delta water. Protecting all the listed species and preserving existing and projected uses of the region’s water is a serious challenge. The complexity of the problem and the difficulty of identifying solutions have been highlighted by a plethora of scientific publications and arguments, in which many qualified and distin- guished experts have reached differing conclusions. Nobody disagrees that en- gineering changes; the introduction of many exotic species, the addition of con- taminants to the system, and the general effects of an increasing human popula- tion have contributed to the fishes’ declines. There are, however, disagreements vii

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viii Preface about the relative contributions of those factors and the appropriate remedies for them. This is the context in which the National Research Council was asked by Congress and the Department of the Interior to help resolve the issue by evaluat- ing the scientific bases of the biological opinions. In response, the NRC ap- pointed a special committee of experts to carry out a complex and challenging study in two phases. In its first phase, the committee was tasked to focus on the scientific bases of the reasonable and prudent alternatives (RPAs) in the two biological opinions. The committee also assessed whether the RPAs might be in conflict with one another, as well as whether other options might be available that would protect the fishes with lesser impacts on other water uses. Finally, we were asked to consider the effects of “other stressors” on the fishes if sufficient time were available. The results of this first-phase analysis are the subject of this report. The committee did consider other stressors, but it did not evaluate them in depth. They will be more thoroughly addressed in a second report, scheduled to be published late in 2011, which will focus on broader issues surrounding at- tempts to provide more sustainable water supplies and to improve the ecological sustainability of the delta, including consideration of what ecological goals might be attainable. The committee met in Davis, California for five days in January 2010. The committee heard presentations from representatives of federal and state agencies and a variety of other experts, and from members of several stakeholder groups and the public (see Appendix D). The information gathering sessions of this meeting were open to the public and widely advertised. The committee sought to hear from as many groups and individuals as possible within the time con- straints. All speakers, guests, and members of the public were encouraged to provide written comments during and after the meeting. All presentations and written materials submitted were considered by the committee as time allowed. The committee thanks all the individuals who provided information. This report was reviewed in draft form by individuals chosen for their di- verse perspectives and technical expertise in accordance with the procedures approved by the NRC’s Report Review Committee. The purpose of this inde- pendent review is to provide candid and critical comments that will assist the NRC in making its published report as sound as possible, and to ensure that the report meets NRC institutional standards for objectivity, evidence, and respon- siveness to the study charge. The review comments and draft manuscript remain confidential to protect the integrity of the deliberative process. We thank the following for their reviews of this report: Joan G. Ehrenfeld, Rutgers University; Mary C. Fabrizio, Virginia Institute of Marine Science; Pe- ter Gleick, Pacific Institute; William P. Horn, Birch, Horton, Bittner & Cherot;

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Preface ix D. Peter Loucks, Cornell University; Jay Lund, University of California, Davis; Tammy Newcomb, Michigan Department of Natural Resources; and Andrew A. Rosenberg, Conservation International. Although these reviewers provided constructive comments and suggestions, they were not asked to endorse the report’s conclusions and recommendations, nor did they see the final draft of the report before its release. The review of this report was overseen by Michael Kavanaugh, Malcolm Pirnie, Inc., who was appointed by the NRC’s Report Review Committee and by Leo Eisel, Brown and Caldwell, who was appointed by the NRC’s Division on Earth and Life Studies. They were responsible for ensuring that an independent examination of this report was conducted in accordance with NRC institutional procedures and that all review comments received full consideration. Responsibility for this report’s final contents rests entirely with the authoring committee and the NRC. I am enormously grateful to my committee colleagues for their diligence, enthusiasm, persistence, and hard work. The schedule for the preparation of this report was short, and without everyone’s engagement, it could not have been completed. I also am grateful to David Policansky, Stephen Parker, Laura Hel- sabeck, Heather Chiarello, Ellen de Guzman, and Susan Roberts of the NRC staff for their efforts in facilitating the committee’s meeting and for their work in helping to get this report completed on schedule in the face of historic snow- storms. California will continue to face great challenges in managing, allocating, and using water, including managing California’s Bay-Delta. We hope the com- mittee’s reports can help in that difficult process. Robert J. Huggett Chair

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Contents Acronyms and Abbreviations............................................................................ xiii SUMMARY......................................................................................................... 1 1 Introduction................................................................................................. 11 System Overview................................................................................. 14 The Present Study ................................................................................ 16 2 The Legal Context of this Report................................................................ 17 Scope of the Committee’s Task ........................................................... 17 Potential Violations of ESA Section 7 and Section 9 .......................... 18 Standards for the Preparation of Biological Opinions ......................... 19 Standards for the Preparation of Reasonable and Prudent Alternatives (RPAs)...................................................................... 20 3 The Life Histories of the Fishes.................................................................. 22 Introduction ......................................................................................... 22 Fishes of the Salmon Family ............................................................... 22 Green Sturgeon .................................................................................... 24 Delta Smelt .......................................................................................... 25 4 Use of Models............................................................................................. 28 Modeling Scenarios ............................................................................. 28 Central Issues Concerning Model Use in the Biological Opinions...... 29 Conclusion ........................................................................................... 40 5 Other Stressors............................................................................................ 42 Introduction ......................................................................................... 42 Contaminants ....................................................................................... 42 Altered Nutrient Loads ........................................................................ 43 xi

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xii Contents Changes in Food Availability and Quality........................................... 43 Introduced Fishes................................................................................. 44 Impediments to Passage, Changes in Ocean Conditions, Fishing, and Hatcheries .............................................................................. 45 Diseases ............................................................................................... 46 Climate Change ................................................................................... 46 Conclusion ........................................................................................... 47 6 Assessment of the RPAs ............................................................................. 48 Introduction ......................................................................................... 48 Delta Smelt .......................................................................................... 50 Salmonids and Sturgeon ...................................................................... 55 Integration of RPAs ............................................................................. 61 Other Possible RPAs............................................................................ 62 Resolving Incompatibilities Between the RPAs .................................. 63 Expectations and Proximate Measures ................................................ 64 RPA Recommendations....................................................................... 64 References.......................................................................................................... 66 APPENDIXES A Committee on Sustainable Water and Environmental Management in the California Bay-Delta: Statement of Task .......................... 79 B Water Science and Technology Board Roster ..................................... 82 C Ocean Studies Board Roster ............................................................... 83 D Speakers at Committee’s Meeting, January 24-28, 2010, Davis............................................................................................. 85 E Biographical Sketches for Members of the Committee on Sustainable Water and Environmental Management in the California Bay-Delta .......................................................... 87

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Acronyms and Abbreviations AF Acre-feet BA Biological Assessment BO Biological Opinion (C)DFG California Department of Fish and Game (C)DWR California Department of Water Resources C.F.R. Code of Federal Regulations Cir Circuit Court (federal system) CVP Central Valley Project CVPIA Central Valley Project Improvement Act DCC Delta Cross Channel DOI (U.S.) Department of the Interior DSM2 Delta Simulation Model II EDT Ecosystem Diagnosis and Treatment ESA Endangered Species Act EWA Environmental Water Account FMT Fall Midwater Trawl (survey) FWS (U.S.) Fish and Wildlife Service HORB Head of Old River Barrier MAF Million acre-feet M&I Municipal and Industrial NAS National Academy of Sciences NMFS National Marine Fisheries Service NOAA National Oceanic and Atmospheric Administration NRC National Research Council OCAP Operations Criteria And Plan OMR Old and Middle River OSB Ocean Studies Board of the NRC PTM Particle-Tracking Model RBDD Red Bluff Diversion Dam RPA Reasonable and Prudent Alternative SWP State Water Project TAF Thousand acre-feet USBR United States Bureau of Reclamation U.S.C. United States Code USGS United States Geological Survey VAMP Vernalis Adaptive Management Plan WSTB Water Science and Technology Board of the NRC X2 Contour line of salinity 2 xiii

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