Historical Distribution and Current Status of Steelhead/Rainbow Trout (Oncorhynchus mykiss) in Streams of the San Francisco Estuary, California Robert A. Leidy, Environmental Protection Agency, San Francisco, CA Gordon S. Becker, Center for Ecosystem Management and Restoration, Oakland, CA Brett N. Harvey, John Muir Institute of the Environment, University of California, Davis, CA This report should be cited as: Leidy, R.A., G.S. Becker, B.N. Harvey. 2005. Historical distribution and current status of steelhead/rainbow trout (Oncorhynchus mykiss) in streams of the San Francisco Estuary, California. Center for Ecosystem Management and Restoration, Oakland, CA. Center for Ecosystem Management and Restoration TABLE OF CONTENTS Forward p. 3 Introduction p. 5 Methods p. 7 Determining Historical Distribution and Current Status; Information Presented in the Report; Table Headings and Terms Defined; Mapping Methods Contra Costa County p. 13 Marsh Creek Watershed; Mt. Diablo Creek Watershed; Walnut Creek Watershed; Rodeo Creek Watershed; Refugio Creek Watershed; Pinole Creek Watershed; Garrity Creek Watershed; San Pablo Creek Watershed; Wildcat Creek Watershed; Cerrito Creek Watershed Contra Costa County Maps: Historical Status, Current Status p. 39 Alameda County p. 45 Codornices Creek Watershed; Strawberry Creek Watershed; Temescal Creek Watershed; Glen Echo Creek Watershed; Sausal Creek Watershed; Peralta Creek Watershed; Lion Creek Watershed; Arroyo Viejo Watershed; San Leandro Creek Watershed; San Lorenzo Creek Watershed; Alameda Creek Watershed; Laguna Creek (Arroyo de la Laguna) Watershed Alameda County Maps: Historical Status, Current Status p. 91 Santa Clara County p. 97 Coyote Creek Watershed; Guadalupe River Watershed; San Tomas Aquino Creek/Saratoga Creek Watershed; Calabazas Creek Watershed; Stevens Creek Watershed; Permanente Creek Watershed; Adobe Creek Watershed; Matadero Creek/Barron Creek Watershed Santa Clara County Maps: Historical Status, Current Status p. 135 San Mateo and San Francisco Counties p. 141 San Francisquito Creek Watershed; Redwood Creek Watershed; Cordilleras Creek Watershed; Belmont Creek Watershed; Laurel Creek Watershed; San Mateo Creek Watershed; Sanchez Creek Watershed; Easton Creek Watershed; Mills Creek Drainage; Colma Creek Watershed San Mateo County Maps: Historical Status, Current Status p. 155 Marin County p. 161 Coyote Creek Watershed; Arroyo Corte Madera Del Presidio Watershed; Corte Madera Creek Watershed; Miller Creek Watershed; Pacheco Creek Watershed; Arroyo San Jose Watershed; Novato Creek Watershed Marin County Maps: Historical Status, Current Status p. 177 Sonoma County p. 183 Petaluma River Watershed; Sonoma Creek Watershed; Schell Creek Watershed Sonoma County Maps: Historical Status, Current Status p. 207 Napa County p. 213 Huichica Creek Watershed; Napa River Watershed; Fagan Creek Watershed; American Canyon Creek Watershed Napa County Maps: Historical Status, Current Status p. 251 Solano County p. 257 Unnamed Creek to Cordelia Slough Watershed; Green Valley Creek Watershed; Suisun Creek Watershed Solano County Maps: Historical Status, Current Status p. 263 Discussion p. 269 Acknowledgements p. 273 Abbreviations & Acronyms p. 275 FOREWARD The document in your hands is the work of generations. When Dr. Robert Leidy first started walking the streams of the East Bay to make field observations of native fishes, he was following paths walked in previous centuries by other biologists. For years Rob made his way along brush- and concrete- covered stream banks, pulling nets and snorkeling in pools, and acquiring the written reports of his predecessors. Now, with the assistance of Gordon Becker and Brett Harvey, these decades of observations have been synthesized and analyzed in a scientifically authoritative manner and made publicly available. Many Bay Area residents are surprised to discover that rainbow trout still inhabit our streams, and that every year steelhead (the ocean-going form of rainbow trout) enter our creeks from the ocean searching for spawning habitat. While the abundance of steelhead has been greatly diminished by the last 50 years of urban development, there still exist Bay Area streams where these magnificent fish make their way upstream to spawn in clear, clean, cold water. Most fisheries scientists believe that with modest modifications to our water supply and flood control infrastructure, and revisions to the operations of certain facilities, we can return steelhead to many places they used to inhabit. Spurred by this knowledge, and the listing of steelhead as threatened pursuant to the Endangered Species Act, citizens and governmental agencies are at work in locations throughout our region on plans to restore these steelhead populations. The Center for Ecosystem Management and Restoration is pleased to provide the scientific information in this document to assist them in these restoration efforts. The technical and political complexity of their task should not be underestimated. The responsibility for protection and restoration of these steelhead populations often rests with government agencies with no official mandate to restore or protect natural resources. These include flood control districts, water supply agencies, and public works departments, and these organizations are struggling to adapt to a new political environment in which they are responsible for managing lands and water resources to protect endangered species. The agencies face inevitable conflicts between their traditional mandates and these new responsibilities, and are working with local stakeholders to address conflicts, build new partnerships, and find supplemental funding opportunities. Certainly, the fish appear willing to do their part. Adult steelhead have been found in downtown Hayward, after swimming 12 miles up a concrete flood control channel. Behind our major dams rainbow trout complete their lifecycle in human-made microcosms. Instead of their downstream migration leading to an oceanic journey of thousands of miles, these fish move downstream to reservoirs, where they live until it is time to return to the upper watershed to spawn. If free to move downstream and back, there is every reason to assume these trout will resume the oceanic round trip of their ancestors, making these wild fish vital resources for restoration. In 2004 the National Marine Fisheries Service proposed that the rainbow trout in the Alameda Creek watershed be included in the officially threatened population, the first designation ever for a population located behind a dam. The report you hold provides for the first time an accessible and credible presentation of where these fish still survive, thanks in part to the maps prepared by the Center’s cartographer David Asbury. Restoration of steelhead in Bay Area watersheds is only just beginning, and their complex life cycle will test our capabilities. To be successful we must integrate management across political boundaries that make no ecological sense, encouraging diverse public and private entities to work together. 3 As with most challenging endeavors, there is much to be gained. The physical beauty and ecological integrity of San Francisco Bay and its watersheds are keys to our region’s economic prosperity and quality of life. As Will Travis, Executive Director of the Bay Conservation and Development Commission, has noted “As the world’s places deteriorate in quality, those that have been protected and enhanced will become even more precious. That is why enhancing the Bay Area’s environment is such an important economic investment.” The return of one of nature’s great spectacles to our counties will enrich the lives of Bay Area residents in non-monetary ways as well. The migratory journey of steelhead from stream to ocean and their indomitable return to their natal habitats have touched the human spirit for generations. Wallace Stegner argued that “something goes out of us as a people” when we drive species to extinction, and there can be no doubt that the restoration of wild creatures in our communities will return something to us and our children. Critical policy decisions are presently being made that will shape the regional landscape for decades to come. Rob and his co- authors have shown that we have the opportunity to choose a path that includes the preservation and restoration of timeless and unique environmental resources for present and future Bay Area residents. Andrew Gunther, Ph.D. Executive Director Center for Ecosystem Management and Restoration Oakland, CA 4 INTRODUCTION Five species of Pacific salmon (genus Oncorhynchus) are known from watersheds tributary to the San Francisco Estuary (Estuary), exclusive of the Sacramento and San Joaquin rivers and their tributaries that drain the Central Valley of California (Leidy 2004). Salmon species either historically or recently recorded from Estuary streams include coho salmon (O. kisutch), chinook salmon (O. tshawytscha), chum salmon (O. keta), pink salmon (O. gorbuscha), and the non-anadromous and anadromous life-history forms of rainbow trout (O. mykiss). Recent status reviews indicate that natural populations of coho and chinook salmon and steelhead within coastal California have declined dramatically over the last 50 years, and populations apparently are continuing to decline in other regions (Brown et al. 1994; CDFG 2002; Myers et al. 1998; NMFS 1996, 1999, 2001). Status reviews have assisted the National Marine Fisheries Service in the identification of over 50 listed Evolutionary Significant Units (ESUs) for West