Santa Clara River Watershed Amphibian and Macroinvertebrate Bioassessment Project Los Angeles & Ventura Counties, California Final Report Prepared for the: Santa Clara River Trustee Council Prepared by: The Wishtoyo Foundation In Association with: South Coast Wildlands Project Team: Frank Hovore Thomas Even Ph.D. Damon Wing Kristeen Penrod Ruben Ramirez Teresa Savaikie November 2008 Santa Clara River Watershed Amphibian and Benthic Macroinvertebrate Bioassessment Project Prepared for the: Santa Clara River Trustee Council Prepared by: The Wishtoyo Foundation In Association With: South Coast Wildlands Project Team: Frank Hovore Thomas Even, Ph.D. Damon Wing Kristeen Penrod Ruben Ramirez Teresa Savaikie Reviewer: Jonathan N. Baskin, Ph.D November 2008 Dedication: Frank Hovore 1945 – 2006 This report is dedicated to our good friend and colleague Frank Hovore, who generously shared his extensive knowledge and passion for natural resources with all who had the benefit of crossing his path. Frank’s hearty and joyous humor will not be forgotten. We are all better for having known him. You will always be missed. Santa Clara River Trustee Council Santa Clara River Watershed Amphibian and Benthic Macroinvertebrate Bioassessment Project Table of Contents Page EXECUTIVE SUMMARY 1 1.0 OVERVIEW & GOALS OF THE PROJECT 2 2.0 PROJECT BACKGROUND INFORMATION 6 2.1 Introduction of Study Area/Survey Areas 6 2.2 Study Area Watershed Description 9 2.3 Study Area Connectivity Description 9 2.4 Existing/Proposed Environmental Impacts 10 2.5 Target Species Natural History 11 3.0 MATERIALS & METHODS 26 3.1 Literature Review 26 3.2 Survey Area Selection 26 3.3 Benthic Macroinvertebrate Surveys 26 3.4 Amphibian Surveys 28 3.5 General Vegetation/Wildlife Surveys 29 3.6 Target Species Habitat Suitability Analysis 29 4.0 RESULTS 29 4.1 Historical Observations of Species Within Study Area 29 4.2 Survey Area Baseline Conditions 34 4.3 Target Species Habitat Suitability Analysis 94 5.0 SUMMARY ANALYSIS 100 5.1 Baseline Conditions 100 5.2 Data Limitations 102 5.3 Direct Impacts 102 5.4 Indirect Impacts 103 5.5 Cumulative Impacts 103 6.0 RECOMMENDATIONS 104 6.1 Restoration Opportunities/Priorities & Benefits 104 6.2 Monitoring Efforts 107 7.0 LITERATURE CITED 112 November 2008 i Santa Clara River Trustee Council Santa Clara River Watershed Amphibian and Benthic Macroinvertebrate Bioassessment Project List of Figures Page 1 – Regional Location Map 7 2 – Vicinity/Survey Site Location Map 8 3 – Target Species Photographs 14 4 – Target Species Photographs 16 5 – Target Species Photographs 19 6 – Target Species Photographs 22 7 – Historical Occurrences of Target Species Within Study Area 30 8 – (1) Santa Clara River Main Stem #1 Photographs 36 9 – (2) Santa Clara River Main Stem #2 Photograph 41 10 – (3) Santa Clara River Main Stem #3 Photographs 46 11 – (4) Santa Clara River Main Stem #4 Photograph 56 12 – (5) Santa Clara River Main Stem #5 Photographs 61 13 – (6) Santa Clara River Main Stem #6 Photograph 66 14 – (7) Santa Clara River Main Stem #7 Photograph 70 15 – (8) Aliso Creek Photographs 74 16 – (9) Escondido Creek Photographs 79 17 – (10) Lower Sespe Creek Photographs 84 18 – (11) Santa Paula Creek Photograph 90 November 2008 ii Santa Clara River Trustee Council Santa Clara River Watershed Amphibian and Benthic Macroinvertebrate Bioassessment Project List of Tables Page 1 – Southern California Threatened, Endangered, or Sensitive Species of 2 Aquatic Ecosystems 2 – Survey Areas 9 3 – Target Species Natural History & Background Summary 11 4 – Survey Area Sample Dates 34 5 – Target Amphibian Species Occurrences/Habitat Suitability at Survey Areas 95 6 – Macroinvertebrate Taxa Occurrences and Functional Group Designations at 98 Survey Areas 7 – Survey Area Restoration Opportunities/Priorities 109 APPENDIX A - Survey Area Bird Species Compendium APPENDIX B - Survey Area Aerial Photographs (1-11) November 2008 iii Santa Clara River Trustee Council Santa Clara River Watershed Amphibian and Benthic Macroinvertebrate Bioassessment Project EXECUTIVE SUMMARY The goals of this project were to survey and map both native and non-native amphibians, their habitats, and associated benthic macroinvertebrate communities to help identify restoration and monitoring priorities along the Santa Clara River. A total of eleven (11) survey areas were selected from within the study area (Santa Clara Watershed). Specifically, seven (7) study areas were located within the mainstem Santa Clara River and four (4) were located in major tributaries including Aliso, Escondido, lower Sespe, and Santa Paula Creeks (Survey Period Mar 2005 – Aug 2006). Three (3) of six (6) target native amphibian species were detected within the eleven (11) study areas including the Pacific chorus frog, California chorus frog and California toad. Western spadefoot are known to be present within the study area but were not documented during the survey efforts. Two (2) introduced predatory amphibian species including the African clawed frog and bullfrog were also documented throughout the majority of the study areas. The benthic macroinvertebrate assessments conducted at each of the study areas resulted in the identification of thirty (30) genera, thirty (30) families of insects, and four (4) non-insect taxa. In general, the abundance and diversity of amphibians and benthic macroinvertebrates is higher in the tributaries of the Santa Clara River than in the mainstem. With the exception of Escondido Creek, which was similar in macroinvertebrate taxonomic composition to the Santa Clara River mainstem, there is a trend toward a diminishing number of aquatic insect families and genera proceeding from the tributaries, Aliso, Sespe, and Santa Paula (mean=17.75 families) to the mainstem of the Santa Clara River (mean=10.43 families). Also, several of the major tributaries, some of which were not surveyed as part of the project remain occupied by federally listed species including the arroyo toad (Castaic, Middle/Upper Piru, Upper Sespe Creeks) and California red-legged frog (San Francisquito Canyon). These species were historically (arroyo toad as recent as 2005) documented within the mainstem of the Santa Clara River. Significant stressors that continue to directly and/or indirectly impact native benthic macroinvertebrates and native amphibian species (several of which likely contributed to the extirpation of the arroyo toad and California red-legged frog from the Santa Clara River floodprone area) include, point source discharge effects to water quality, loss of upland amphibian habitat (urbanization and agricultural uses), unnatural releases from reservoirs which alter geomorphology, reservoir impacts on population fragmentation (arroyo toads in upper Castaic, middle and upper Piru Creeks), invasive plant species, mining, and groundwater extraction (can result in reducing duration of pooling needed for the completion of amphibian metamorphosis). Based on the results of the study, recommendations include implementing a program for population control of African clawed frogs and bullfrog, continuation of programs for controlling introduced plants (Arundo donax and Tamarisk species), encouraging riparian vegetation restoration in all drainages and upland vegetation within 1 km (0.6 mi) of streams and rivers, restoration of the natural historic flow regime or creation of a regime that provides maximum benefit for native biodiversity, development of a management and monitoring program based on Total Maximum Daily Load standards, and the minimization of development impacts on aquatic habitats primarily focusing on the use of riparian buffer zones. Monitoring efforts should include developing a long-term water quality/target species monitoring program, groundwater level monitoring program throughout the watershed to determine to what November 2008 1 Santa Clara River Trustee Council Santa Clara River Watershed Amphibian and Benthic Macroinvertebrate Bioassessment Project extent extraction is having on the successful recruitment (successful breeding) of amphibians throughout the floodprone area, initiation of focused surveys for the western spadefoot, arroyo toad and California red-legged frog to determine presence/absence at select sites, and implementation of a public environmental education program. Continued support for existing programs that promote water conservation, recycling, water quality protection, and respect for our natural resources (while protecting the publics passive use of open space areas) will represent one of the most important approaches to assuring that native benthic macroinvertebrates and amphibians persist in the Santa Clara Watershed. 1.0 OVERVIEW & GOALS OF THE PROJECT Worldwide declines in amphibian populations are at the forefront of the global biodiversity crisis and southern California is a hotspot of amphibian declines (Jennings 1988, Fellers and Drost 1993, Jennings and Hayes 1994, Drost and Fellers 1996, Fisher and Shaffer 1996, Davidson et al. 2002). The primary factors contributing to amphibian population declines are habitat loss and degradation (Alford and Richards 1999, Blaustein and Kiesecker 2002). It has been estimated that as much as 90% of the historic riparian habitat in southern California has been eliminated at the hand of anthropocentric-induced impacts and pressures. Coastal watersheds, such as the Santa Clara River Watershed, have suffered due to dams, diversions, channelization, urban and agricultural development, livestock grazing, and other disturbances (Dennis et al. 1984, Bell 1997). In Los Angeles County alone, over 97% of the wetlands once present are now gone, and the wetland and riparian communities remaining are intensely threatened. This significant loss of habitat has been accompanied by a decline in wildlife populations that depend wholly or in part on riparian systems. The ninth annual report of the U.S. Council on Environmental Quality (1978) states “no ecosystem is more essential than the riparian system to the survival of the nation’s fish and wildlife” (Faber et al. 1989). Krueper (1992) estimates that wetland and riparian habitat occupies less than 1% of the total land area in the western U.S., yet is critical for up to 80% of terrestrial vertebrate species. Many aquatic vertebrate species that depend on low-elevation (<3,000') riparian habitats are now Federally- and/or State-listed as endangered, threatened, or sensitive (Table 1; USDA 2000). Riparian habitats are truly among the rarest and most sensitive ecosystem types in the western United States. Table 1 Southern California Threatened, Endangered, or Sensitive Species of Aquatic Ecosystems Species <3,000 ft California red-legged frog Yes Foothill yellow-legged frog Yes Mountain yellow-legged frog No Coast Range newt Yes Arroyo toad Yes Santa Ana sucker Yes Santa Ana speckled dace Yes Arroyo chub Yes Southern steelhead Yes Shay Creek stickleback No Unarmored threespine stickleback Yes California red-sided garter snake Yes Southwestern pond turtle Yes November 2008 2 Santa Clara River Trustee Council Santa Clara River Watershed Amphibian and Benthic Macroinvertebrate Bioassessment Project Development and alteration of stream and river channels, associated terraces, and upland habitats are major factors contributing to the loss of aquatic and semi-aquatic amphibians and reptiles. Rapid growth in agriculture, industry, and urban development has resulted in dramatic direct and indirect impacts to the Santa Clara River and its tributaries. Degradation from the cumulative impacts of polluted runoff, concrete channelization, mining, water treatment plants, grading and infill, and other contributors such as the ARCO pipeline oil spill threatens the inhabitants of this wild river system. For instance, excessive concentrations of suspended sediment can outright kill aquatic organisms and impair the productivity of the River (Trombulak and Frissell 2000). The Santa Clara River Watershed is under intense development pressure, putting native amphibians at risk of extinction. Exotic plant and wildlife species in both aquatic and terrestrial habitats have substantially degraded and disrupted the natural communities that native amphibians depend upon for survival. Numerous introduced species are now abundant in the riparian communities of southern California; some were intentionally introduced for erosion control, recreation for anglers, or mosquito abatement, while others, such as ornamentals, have escaped cultivation due to their adaptive physiology. Introduced species have disrupted the ecological integrity of entire watersheds which has had profound effects on species that are adapted to and dependent upon these natural communities. As these communities become invaded and dominated by non-native species they become less able to support native species. Dudley and Collins (1995) conducted a statewide analysis of non-indigenous species, and concluded that the South Coast Bioregion has more non-native species than any other ecoregion in California. The invasion of alien species to riparian systems is detrimental to amphibians (Kiesecker 2003, Kats and Ferrer 2003). Non-native species can harm amphibians through competition (Kiesecker 2003), disease transmission (Kiesecker et al. 2001, Blaustein and Kiesecker 2002), and predatory interactions (Kats and Ferrer 2003). Introduced fish are evidently the most widespread predators on amphibians (Stebbins and Cohen 1995). Most non-native fish have been introduced to lakes and ponds to provide game for sport fishermen (Cory 1963, Knapp 1996, Stein et al. 2000, Kats and Ferrer 2003), though they can spread easily to stream and river systems during major flood events (Bradford 1989). Even hatchery-reared salmonid fishes may eat native amphibians (Bradford 1989) or infect them with pathogens (Blaustein et al. 1994, Kiesecker et al. 2001). Mosquitofish (Gambusia) have been introduced into many systems because of their effectiveness at controlling mosquito populations (Miura et al. 1979, Bence 1988) but their diet also includes amphibian larvae (Webb and Joss 1997, Goodsell and Kats 1999, Kats and Ferrer 2003). Crayfish (Procambarus clarkia) are also effective predators of amphibians (Gamradt and Kats 1996), as are bullfrogs (Rana catesbeiana) (Zweifel 1955, Beringer and Johnson 1995, Kiesecker and Blaustein 1997, Kats and Ferrer 2003). These non- native predators can drive local amphibian populations to extinction (Bradford 1991, Bradford et al. 1994, Gamradt and Kats 1996, Matthews et al. 2001). Arundo, or giant reed (Arundo donax) is an introduced plant species that has become established in many parts of the Santa Clara River Watershed. This exotic plant is particularly invasive, eliminating native plants and significantly changing the character of the habitat for wildlife (Faber et al. 1989). Arundo donax is now widely distributed in moist places in California, and has displaced extensive amounts of native vegetation along streams and watercourses, particularly at elevations below 1,000 feet (Faber et al. 1989). It is extremely invasive, competitive, and difficult to control in riparian communities, and provides neither food nor nesting habitat for native animals (Bell 1997). This exotic plant compromises the ability of riparian communities to support native species because it doesn’t provide the physical, November 2008 3 Santa Clara River Trustee Council Santa Clara River Watershed Amphibian and Benthic Macroinvertebrate Bioassessment Project structural, or chemical characteristics necessary for proper ecosystem function. Exotic plant invasion significantly diminishes habitat quality and quantity (Faber et al. 1989). Several contaminants may also adversely affect amphibian populations, such as pesticides, herbicides, fungicides, fertilizers, and numerous pollutants (Sparling et al. 2000, Blaustein and Kiesecker 2002). These contaminants can cause direct mortality, have an effect on behavior, reduce growth rates, act as endocrine disrupters or induce immunosuppression (Alford and Richards 1999). Agriculture is a major land use, particularly in the lower watershed. In 1998 alone, California farmers used over 90 million kg of pesticide-active ingredients (Department of Pesticide Regulation 1998). Researchers have documented the transport and deposition of pesticides from the agriculturally intensive Central Valley to the adjacent Sierra Nevada Mountains (Cory et al. 1970, Datta et al. 1998). Even low levels of pesticides can cause fatalities in amphibians (Taylor et al. 1999, Davidson et al. 2002). Ground water pumping has also drastically altered the hydrology of the Santa Clara River and its tributaries and has likely triggered a substantial reduction in riparian vegetation. There are a number of wells that extract groundwater from the aquifers at rates greater than 100 gallons per minute and several small volume private wells scattered throughout the watershed. Concerns over groundwater supplies arose as early as the 1920s (Schwartzberg and Moore 1995). Groundwater levels have been declining ever since due to an increase in industrial, commercial and residential uses in conjunction with prolonged drought (AMEC 2004). Groundwater supplies are now at record lows, with several wells in the upper watershed at catastrophically low levels. Water quality on the main stem and several tributaries has also been degraded are listed as impaired under Section 303(d) of the Clean Water Act due to excessive total dissolved solids, sulfate and chloride in 2006 (RWQCB). Total dissolved solids are measured as the amount of material that is dissolved in water and can include carbonate, bicarbonate, chloride, sulfate, phosphate, nitrate, calcium, magnesium, sodium, organic ions, and other ions. These listings make these riparian stretches eligible for the development of intensive management plans called Total Maximum Daily Load (TMDL) plans. TMDLs are implemented by the Regional Water Quality Control Board, which evaluates the cause of water quality deterioration and then enacts an implementation plan to return water quality to targeted values. Other water quality efforts either completed or in progress include development of a chloride TMDL (Total Maximum Daily Load) for the upper reach of the River, a nutrient TMDL, and on-going NPDES permit related monitoring (AMEC 2004). Amphibians are considered ecological barometers of ecosystem and watershed health because they experience both aquatic and terrestrial stressors (Blaustein and Wake 1995, Blaustein and Kiesecker 2002). Amphibians, such as the arroyo toad (Bufo californicus), are ideal aquatic habitat quality indicators because of their dependence on riparian and adjacent upland habitat, high water quality, and native ants. The arroyo toad is known to utilize upland habitats up to 1.2 km beyond the riparian zone (Holland and Sisk 2001a). Similarly, Western spadefoot toad (Spea hammondii) requires seasonal pools for breeding but may travel hundreds of meters outside the breeding area to forage and reach underground refugia. While semi-aquatic reptiles, such as pond turtle (Actinemys marmorata pallida) and two-striped garter snake (Thamnophis hammondii) require nearby uplands for nesting and over wintering movement requirements (Rathburn et al. 1992, Rathburn et al.1993). This seasonal migration between wetland and upland habitats makes these species vulnerable to roadkill (Rosenberg et al. 1997). The remaining riparian communities in the watershed are crucial to the survival of native amphibian populations. November 2008 4