RESIDENT SPECIES STUDY SANTA CLARA RIVER ESTUARY VENTURA WATER RECLAMATION FACILITY NPDES PERMIT NO. CA0053651, CI-1822 Prepared for: CITY OF SAN BUENAVENTURA Ventura, CA Prepared by: ENTRIX, INC. Ventura, CA Project No. 325403 September 17, 2002 RESIDENT SPECIES STUDY SANTA CLARA RIVER ESTUARY VENTURA WATER RECLAMATION FACILITY NPDES PERMIT NO. CA0053651, CI-1822 Prepared for: CITY OF SAN BUENAVENTURA 1400 Spinnaker Drive Ventura, CA 93002 Prepared by: ENTRIX, INC. 2140 Eastman Avenue, Suite 200 Ventura, California 93003 Project No. 325403 September 17, 2002 TABLE OF CONTENTS Page List of Preparers................................................................................................................. vi Executive Summary........................................................................................................... ix 1.0 Introduction.......................................................................................................... 1-1 1.1 Regulatory History................................................................................... 1-3 1.1.1 1995 NPDES Permit .................................................................... 1-3 1.1.2 Phase 1 Report ............................................................................. 1-4 1.1.3 Phase 2 Report ............................................................................. 1-4 1.1.4 Phase 3 Report ............................................................................. 1-5 1.1.5 Studies Supplemental to the Phase 3 Report................................ 1-5 1.1.5.1 Metals Translator Study............................................. 1-6 1.1.5.2 Resident Species Study.............................................. 1-6 1.2 Objectives and Approach of the Resident Species Study ........................ 1-6 1.3 Report Organization................................................................................. 1-8 2.0 Environmental Setting of the Santa Clara River Estuary..................................... 2-1 2.1 Species Composition in Estuaries............................................................ 2-1 2.2 Physical Setting of the Santa Clara River Estuary................................... 2-2 2.3 Habitat Conditions in the Santa Clara River Estuary............................... 2-3 2.3.1 Vegetation.................................................................................... 2-3 2.3.2 Wildlife ........................................................................................ 2-4 2.3.3 Previous Invertebrate Studies ...................................................... 2-4 3.0 Methods ............................................................................................................... 3-1 3.1 Field Data Collection ............................................................................... 3-1 ii 3.1.1 Benthic Macroinvertebrate Surveys............................................. 3-1 3.1.2 Environmental Parameters........................................................... 3-3 3.1.3 Vegetation.................................................................................... 3-3 3.1.4 Sorting and Taxonomy Protocol .................................................. 3-3 3.1.4.1 Materials .................................................................... 3-3 3.1.4.2 Methods ..................................................................... 3-4 3.1.4.3 Elutriation .................................................................. 3-4 3.1.4.4 Final Sorting .............................................................. 3-5 3.1.4.5 Subsampling............................................................... 3-5 3.1.4.6 Taxonomy .................................................................. 3-5 3.1.5 Use of Existing Data .................................................................... 3-5 3.1.6 Data Analysis............................................................................... 3-6 3.1.7 Literature Reviews....................................................................... 3-8 4.0 Results.................................................................................................................. 4-1 4.1 Physical and Chemical Characteristics During the Study Period ............ 4-1 4.1.1 Natural Hydrologic Influences..................................................... 4-1 4.1.1 Water Quality............................................................................... 4-1 4.1.2 Sediment Data.............................................................................. 4-2 4.2 Benthic Macroinvertebrate Survey and Data Analysis Results ............... 4-3 4.2.1 Dominant Taxa............................................................................. 4-4 4.2.2 Uncommon Taxa.......................................................................... 4-5 4.2.3 Community Structure................................................................... 4-6 4.2.4 Relationship to Physical Parameters............................................ 4-6 4.2.5 Cluster Analysis........................................................................... 4-7 4.2.6 Ordination .................................................................................... 4-7 iii 4.2.7 Relationships with USFWS Data................................................. 4-8 4.3 Salinity Tolerance Review of Estuary Taxa .......................................... 4-10 5.0 Comparison of the Santa Clara River Estuary to Other Estuaries in the Southern California Bight.................................................................................... 5-1 5.1 Mugu Lagoon........................................................................................... 5-1 5.1.1 Benthic Invertebrate Studies........................................................ 5-2 5.2 Malibu Lagoon......................................................................................... 5-2 5.2.1 Benthic Invertebrate Studies........................................................ 5-2 5.3 Santa Margarita Estuary........................................................................... 5-3 5.3.1 Benthic Invertebrate Studies........................................................ 5-3 5.4 Batiquitos Lagoon.................................................................................... 5-3 5.4.1 Benthic Invertebrate Studies........................................................ 5-4 5.5 San Dieguito Lagoon ............................................................................... 5-4 5.5.1 Conditions During Benthic Invertebrate Studies ......................... 5-4 5.6 Los Penasquitos Lagoon .......................................................................... 5-5 5.6.1 Benthic Invertebrate Studies........................................................ 5-6 5.7 Tijuana Estuary ........................................................................................ 5-6 5.7.1 Benthic Invertebrate Studies........................................................ 5-7 5.8 Comparisons with the Santa Clara River Estuary.................................... 5-7 6.0 Comparison of Santa Clara River Invertebrates to Those Used by EPA in Establishing Ambient Water Quality Criteria...................................................... 6-1 6.1 Overview of the Ambient Water Quality Criteria Method ...................... 6-1 6.2 EPA Basis for Development of the Copper Ambient Water Quality Criteria ..................................................................................................... 6-3 6.2.1 Copper Freshwater Criteria.......................................................... 6-3 6.2.2 Overview of the Copper Saltwater Criteria ................................. 6-4 iv 6.3 Selection of Ambient Water Quality Criteria for the Santa Clara River Estuary ........................................................................................... 6-4 6.3.1 Similarity in Salinity Tolerances ................................................. 6-4 6.3.2 Taxonomic Overlap ..................................................................... 6-5 7.0 Discussion............................................................................................................ 7-1 7.1 Benefits of Continuing Discharge............................................................ 7-1 7.2 Integration of Resident Species Study Results ........................................ 7-1 7.3 Final Recommendations........................................................................... 7-2 8.0 Invertebrate Taxonomy References ..................................................................... 8-1 9.0 General References .............................................................................................. 9-1 Appendix A. Physical and Chemical Survey Results Appendix B. Macroinvertebrate Survey Results Appendix C. U. S. Fish and Wildlife Macroinvertebrate Results Appendix D. Salinity Tolerance Literature Review v LIST OF PREPARERS Matthew Carpenter, Study Project Manager B.S., Forestry and Natural Resources, Environmental Management concentration, California Polytechnic State University, San Luis Obispo, 1995 Daniel Tormey, Ph.D., Senior Technical Contributor-Technical Co-Lead Ph.D., Geology and Chemistry, Massachusetts Institute of Technology, 1989 B.S., Civil Engineering and Geology, Stanford University, 1983 Theodore Donn, Jr., Ph.D., Senior Technical Contributor-Statistical Analysis Ph.D., Zoology, University of New Hampshire, 1983 B.A., Biology, Clark University, 1977 Jennifer