Swanson Hydrology & Geomorphology D.W. ALLEY & Associates 115 Limekiln St. Santa Cruz, CA 95060 P.O. Box 200 Brookdale, CA 95007 Phone 831-427-0288 / fax 427-0472 Ph: 831-338-7971 FAX: 831-338-6045 www.swansonh2o.com [email protected] FINAL REPORT SAN LORENZO RIVER SALMONID ENHANCEMENT PLAN Fisheries Enhancement Strategy for the San Lorenzo River submitted to Santa Cruz County Environmental Health Services by Donald Alley, D.W. ALLEY &Associates John Dvorsky, Swanson Hydrology & Geomorphology John Ricker, Santa Cruz County Environmental Health Kristen Schroeder, Santa Cruz County Planning Dr. Jerry Smith, San Jose State University March 2004 San Lorenzo River Salmonid Enhancement Plan Swanson Hydrology & Geomorphology D.W. ALLEY & Associates Page ES-1 EXECUTIVE SUMMARY BACKGROUND AND INTRODUCTION In order to update the fisheries section of the San Lorenzo River Watershed Management Plan Update, the County of Santa Cruz, with funding from the California Coastal Conservancy, contracted with Swanson Hydrology & Geomorphology, D.W. ALLEY and Associates, and Dr. Jerry Smith to develop a technical document that outlines the primary impacts to salmonid resources within the San Lorenzo River and tributaries and outlines a set of measures and recommendations needed to enhance the existing steelhead population and restore the coho salmon population. Over the last several years, a considerable amount of attention has been paid to salmonid populations and habitat conditions on the San Lorenzo River due to historical accounts that suggest a rapid decline in fish numbers since the 1960’s. The California Department of Fish and Game (CDFG) estimated that 20,000 adult steelhead were present in the San Lorenzo River prior to 1965 (Johansen, 1975). In the mid-1960’s, CDFG estimated that 19,000 adult steelhead occurred in the San Lorenzo River. Recent estimates by the NOAA Fisheries, made in 1996, put the number of adults spawning in the San Lorenzo River at 500. Unfortunately, estimates of historic adult steelhead numbers were based on conjecture and lack supportable scientific data. Most of the estimates were based on creel census data, which are inadequate to obtain accurate estimates of adult numbers and are more reflective of the extensive planting program in the San Lorenzo River rather than natural production. Scientifically supportable juvenile population and density estimates did not occur on the San Lorenzo until 1981 when Dr. Jerry Smith, with assistance from Donald Alley, conducted habitat surveys and sampling site density estimates on steelhead-bearing streams throughout Santa Cruz County (Smith, 1982). Comprehensive habitat condition and population estimates were continued in 1994 by D.W. ALLEY and Associates and have been monitored every year since (Alley, 1995-2001). These data suggest fairly stable steelhead populations between 1981 to present with year-to-year variations dependent upon sedimentation, streamflow, and habitat conditions in the River. Recent population estimates indicate declines in key reaches such as the Middle River. Historic and present population estimates suggest an even darker picture for coho salmon. Though little data exist on watershed-wide adult numbers, coho salmon were sampled and identified in the San Lorenzo River at least until 1981 (Smith, 1982). Recent surveys of fish numbers, conducted since 1994 have not reported a single coho salmon individual (Alley, 1994-2001). According to NOAA Fisheries, coho salmon are thought to have been extirpated from the San Lorenzo River through a combination of habitat loss and drought conditions in the late 1980’s, and early 1990’s (J. Ambrose, NOAA Fisheries, personal comm.). The severe drought of 1976-77 also had impacts. Based on these estimates of declining fish numbers over the last 35 years the NOAA Fisheries designated San Lorenzo River steelhead and coho salmon (as part of the Central Coast Evolutionarily Significant Unit) as two species that are experiencing a significant decline in numbers, enough to warrant the federal government to list them as threatened under the Endangered Species Act. Coho salmon is state listed as an Endangered Species south of the San Francisco Bay. The federal listing of steelhead and coho salmon in the San Lorenzo River occurred as a result of regional concerns about the decline of these two species in a wide geographic region. Prior to the listing, research, data collection and monitoring of these populations and the physical conditions that affect their habitat have occurred since the early to mid-1990’s (Alley, 1994-2002; Hecht and Kittleson, 1998; Swanson and Dvorsky, 2001). The focus of this research has been to understand population dynamics in relation to habitat conditions, and erosion and sedimentation patterns throughout the watershed. Following the listing of steelhead and coho salmon, development of a document that synthesizes existing biological and physical data into comprehensive plan for enhancement and restoration of these populations became a top San Lorenzo River Salmonid Enhancement Plan Swanson Hydrology & Geomorphology D.W. ALLEY & Associates Page ES- 2 priority. Through this analysis, key limiting factors contributing to the decline of steelhead and coho salmon could be identified, with recommendations made for habitat improvement. HABITAT AND POPULATION ASSESSMENT EFFORTS Limited standardized historical data existed prior to 1981 to describe habitat conditions and populations for salmonids on the San Lorenzo River. In 1994, the City of Santa Cruz Water Department and San Lorenzo Valley Water District initiated funding for a long-term monitoring program designed to assess the status of salmonids in the San Lorenzo River. Santa Cruz County joined in funding the effort in 1998. Based on habitat evaluation and fish sampling conducted through this program, data are available from 1994 to 2001 in the mainstem (Alley, 1995-2002) along with data collected in 1981 (Smith, 1982) with expanded data collection beginning in 1998 to include sampling in the tributaries. Random and non- random sampling was conducted in 2002 by H.T. Harvey and Associates (2003). Methods: Values and Limitations The methods used in assessing habitat and fish populations are described in Appendix A and in the referenced literature. Habitat conditions were surveyed by representative subsampling of the total available habitat. Sampling sites were selected from habitat-typed segments of reaches using a field- based determination of “average habitat conditions”. This approach is called the Average Habitat Quality method (AHQ). Fish density estimates in specific habitat types of representative subsamples were then used to extrapolate fish numbers for the rest of the reach, using the habitat proportio ns determined from the habitat-typed segments. Sampling sites were repeated from year to year, except in cases where average habitat conditions changed considerably, based on annual habitat typing. This sampling protocol is based on the following assumptions (discussed further in Appendix A): • It is the density of smolt-sized steelhead within the juvenile population that primarily determine the return of adult steelhead to the stream, • There is a positive relationship between habitat quality and juvenile steelhead numbers, • The density of smolt-sized juvenile steelhead (and less so for smaller juveniles), in relation to habitat quality (i.e.-poor, average, high), is approximately linear and, therefore, average habitat (in terms of water depth and escape cover) supports an average number of smolt- sized juvenile fish, and • The available habitat is saturated with smolt-sized juvenile steelhead in most years and most stream reaches. • Most juveniles captured during fall sampling reside at the site of capture for most of the dry season. The representative reach approach using AHQ was selected over the random sampling approach to maximize sampling coverage throughout the watershed with limited funding and to provide a consistent dataset from year to year to assess population trends. Due to the lack of a statistically based random sampling effort, the statistical significance and degree of confidence in the estimated fish numbers is difficult to assess. Given these limitations, the same-site, year to year comparisons of fish density, size and age class are useful to assess trends in juvenile production, evaluate reach to reach variability, assess limiting factors, and evaluate the relative effects of changes in habitat conditions to guide watershed management efforts. In addition, when the same sites are sampled between years, the statistically powerful t-test has been performed to evaluate statistical significance of year-to-year variations in fish densities at sampling sites. The fish population estimates contained in this report could possibly be further refined or modified through more detailed assessments, random sampling, adult monitoring, and/or downstream migrant monitoring, although many of these methods also have limitations of cost and/or effectiveness. San Lorenzo River Salmonid Enhancement Plan Swanson Hydrology & Geomorphology D.W. ALLEY & Associates Page ES- 3 In 2002, the City of Santa Cruz hired H.T. Harvey and Associates to conduct salmonid sampling in the San Lorenzo River and tributaries. Sampling in the mainstem and tributaries used non-random sampling, which was intended to be comparable to methods used by D.W. ALLEY & Associates (1998-2001). In addition, random sampling was conducted in the middle segment of the mainstem