I I I REVISED 1 STREAMM AINTENANCPER OGRAM I BIOLOGICAALS SESSMENT I I I I I I I I I Santa Clara Valley Water District I 5750 AImaden Expressway San Jose, California 95118-3686 I I September 2001 I Santa Clara Valley Water District B 1 I TABLE OF CONTENTS I Page LOCATION ..................................................................... 1 I CONTACTPERSON ............................................................. 1 I INTRODUCTION ................................................................ 1 CRITICAL HABITAT ............................................................. 1 I CONSULTATIONTODATE ....................................................... 3 I CURRENTMANAGEMENTDIRECTION ............................................ 5 DESCRIPTION OF THE PROPOSED ACTION ........................................ 6 I Project Location ............................................................. 6 Work Projections and Planning Horizon .......................................... 7 SedimentRemoval ........................................................... 8 I VegetationManagement ...................................................... 9 Bankprotection ............................................................ 15 Minor Stream Maintenance Activities ........................................... 17 T Mitigation Incorporated Into the Project ......................................... 19 Best Management Practices ............................................. 19 Mitigation for Bank Protection ........................................... 20 I Compensatory Stream Vegetation and Special-Status Species Mitigation .......... 21 ACTION AREA ................................................................. 22 1 SURVEYS AND MONITORING PERFORMED BY THE DISTRICT ..................... 22 Special-Status Plant Surveys .................................................. 23 1 FisheriesSurveys ........................................................... 23 Fish Habitat Categories ...................................................... 23 California Red-Legged Frog Surveys ........................................... 27 1 Birdsurveys ............................................................... 27 SPECIES ACCOUNTS AND STATUS OF THE SPECIES IN THE ACTION AREA ..........2 7 I Salt Marsh Harvest Mouse .................................................... 27 Western Snowy Plover ....................................................... 28 California Clapper Rail ...................................................... 28 I Least Bell ,sVi.reo .......................................................... 29 SanFranciscoGarterSnake ................................................... 29 CaliforniaRed-LeggedFrog .................................................. 30 i California Tiger Salamander .................................................. 31 Steelhead ................................................................. 31 ChinookSalmon ........................................................... 34 8 Bay Checkerspot Butterfly .................................................... 36 i 1 I I Page Tiburonpaintbrush ......................................................... 36 i CoyoteCeanothus .......................................................... 37 Santa Clara Valley Dudleya ................................................... 37 Metcalf Canyon Jewelflower .................................................. 37 1 CaliforniaSea-Blite .......................................................... 38 Mount Hamilton Thistle ...................................................... 38 1 EFFECTS ...................................................................... 38 Salt Marsh Harvest Mouse .................................................... 38 Western Snowy Plover ....................................................... 39 1 CaliforniaClapperRail ...................................................... 39 LeastBell’sVireo .......................................................... 40 SanFranciscoGarterSnake ................................................... 41 1 CaliforniaRed-LeggedFrog .................................................. 41 California Tiger Salamander .................................................. 43 Steelhead ................................................................. 44 1 ChinookSalmon ........................................................... 49 Bay CheckerspotButtemy .................................................... 50 Tiburon Paintbrush. Coyote Ceanothus. Santa Clara Dudlyea. Metcalf Canyon Jewelflower 1 and Mt . Hamilton Thistle ..................................................... 53 CaliforniaSea-Blite ......................................................... 54 . . . Compensatory Mitigation .................................................... 54 Interrelated and Interdependent Actions ......................................... 58 CUMULATIVEEFFECTS ........................................................ 59 Cumulative Effects of Stream Maintenance ...................................... 59 Cumulative Effects with Other District Projects ................................... 60 Cumulative Effects with Non- District Projects ................................... 60 ANALYSIS OF ALTERNATE ACTION .......................... 61 Comparison of Project Alternatives .......................... 66 CONCLUSION ANDDETERMINATION ........................................... 67 LITERATURECITED ........................................................... 68 LIST OF CONTACTSlCONTRIBUTORS/PREPARERS ................................ 11 .. I1 TABLES All tables are attached at the end of report. TABLE 1 Special Status Species Herbicide Exposure Categories TABLE 2 Special-Status Species Rodenticide Use Limitations Code TABLE 3 Compensatory Stream Vegetation and Special-Status Species Mitigation TABLE 4 Fish Habitat By Basin TABLE 5 Fish Habitat By Channel Type TABLE 6 Historical Occurrences of San Francisco Garter Snakes in Santa Clara County TABLE 7 Potential Effects on California Clapper Rail TABLE 8 Habitat Observations in Pajaro River Watershed Which May Support Least Bell’s Vireos TABLE 9 Potential Effects on California Red-legged Frog TABLE 10 Potential Effects on California Tiger Salamanders TABLE 11 Channel Maintenance Activities Occurring in Different Fish Habitat Types in Santa Clara Basin and Pajaro River Basin TABLE 12 Summary of In-Channel Vegetation Impacts in Acres TABLE 13 Other Future District Projects in Creeks TABLE 14 Definition of Alternatives TABLE 15 Cost Comparison of Alternatives TABLE 16 Potential Flooding Area Under the No Work Alternative TABLE 17 Alternatives Comparison of Initial and Long-Term Stream Vegetation Impacts FIGURES All figures are attached at the end of report. FIGURE 1 Streams and Canals in District Jurisdiction FIGURE 2 Stream Maintenance Program Resource Protection Protocol FIGURE 3 Proposed Stream Vegetation Mitigation Sites FIGURE 4 Fisheries Present in Streams Within the Jurisdiction of the Santa Clara Valley Water District FIGURE 5 California Red-Legged Frog in the Multi-Year Stream Maintenance Program Area FIGURE 6 Salt-Marsh Harvest Mouse in the Multi-Year Stream Maintenance Program Area FIGURE 7 Snowy Plover Nest Locations in the Multi-Year Stream Maintenance Program Area FIGURE 8 California Clapper Rail in the Multi-Year Stream Maintenance Program Area FIGURE 9 Least Bell’s Vireo in the Multi-Year Stream Maintenance Program Area FIGURE 10 San Francisco Garter Snake Occurrences in the Multi-Year Stream Maintenance Program Area FIGURE 11 California Tiger Salamander inthe Multi-Year Stream Maintenance Program Area FIGURE 12Extant Populations and Critical Habitat for the Bay Checkerspot Butterfly in the Multi- Year Stream Maintenance Program Area FIGURE 13 Multi-Year Stream Maintenance Program Reduced Work Alternative - All Activities ... 111 ATTACHMENTS Attachment A - Best Management Practices List Attachment B - Guidelines for Reduction of Maintenance Activities in Unmodified Streams Attachment C - Programmatic Impact Assessment and Mitigation for Routine Bank Protection Activities Attachment D - Sensitive Plants, Wildlife, and Fish at Your Worksite Attachment E - Compensatory Mitigation Site Selection Criteria for California Red-legged Frogs Attachment F - DrybacWish Relocation Operation Guidelines Attachment G - Urban Runoff Pollution Prevention Efforts by District - . Attachment H Comment Letters from US Fish and Wildlife Service and National Marine Fisheries Service iv STREAM MAINTENANCE PROGRAM BIOLOGICAL ASSESSMENT-SANTA CLARA VALLEY WATER DISTRICT LOCATION Santa Clara County, California CONTACT PERSON Cindy Roessler, Project Manager Phone: (408) 265-2607, extension 2765 E-mail: [email protected] INTRODUCTION The purposeofthis BiologicalAssessment(BA) is to review the SantaClaraValley WaterDistrict's (District or SCVWD) Stream Maintenance Program (SMP) in sufficient detail to determine to what extent the proposed action may affect any of the threatened, endangered, candidate, or special concern species under the Federal Endangered Species Act (ESA) as listed below. The analysis is based on the proposed action presented within three documents: the SMP (SCVWD March 2001), Draft Environmental Impact Report (DEIR) fortheSMP(SCVWDMarch 2001). and theFinalEnvironmental Impact Report(FEIR)fortheSMP (SCVWD August 2001). This BA is prepared in accordance with legal requirements set forth under Section 7 of the Endangered Species Act (ESA) (16 U.S.C. 1536 (c)). This list of species under consideration was complied using the following resources: (1) lists of species provided by the US. Fish and Wildlife Service (USFWS) on November 28, 2000 (county list, to Doug Padley, District) andNovember 13,2000 (by watersheds, to Cindy Roessler, District); (2) Department ofFish and Game's CaliforniaNatural Diversity Data Base (CNDDB); (3)CaliforniaNative Plant Society Inventory of Rare or Endangered Vascular Plants of California (5" edition, electronic version, 2000); (4) information provided by District biologists and local experts; and (5) consultation with regulatory agency personnel. CRITICAL HABITAT The proposed action addressed within this BA falls within Critical Habitat for bay checkerspot butterfly. Final ruling on Critical Habitat for the bay checkerspot butterfly was established by USFWS on April 30, 2001 ' The proposed action also falls within Critical Habitat for steelhead. Final ruling on Critical Habitat for steelhead was established by National Marine Fisheries Service (NMFS) on February 16,2000. In addition, the Coyote Creek and Guadalupe River Hydrological Units are identified as Essential Fish Habitat for chinook salmon. Critical habitat for California red-legged frogs (USFWS, March 13, 2001) does not fall within the action area. Critical habitat designations for western snowy plover (USFWS, December 7, 1999) and least Bell's vireo (USFWS,F ebruary 2, 1994) do not include any areas in Santa Clara County. 1 I Jt Stream Maintenance Program Biological Assessment September 2001 I The species considered in this document are: Threatened, Endangered, Candidate, and Special Concern Species I I _. MAMMALS Saltmarsh harvest mouse Reithrodontomys E I I raviventris - + BIRDS Western snowy plover Charadrius T 1 alexandrinus nivosus - ~~~ ~~~ California clapper rail Rallus longirostris E 1 obsoletus - Least Bell’s vireo Vireo bellii pusillus E I REPTILES San Francisco garter snake Thamnophis sirtalis E tetrataenia I AMPHIBIANS California red-legged frog Rana aurora draytonii T 1 California tiger salamander Ambystoma C califomiense - 1 ~~ Steelhead (South/Central Oncorhynchus mykiss T California Evolutionary Significant Unit (ESU) and I Central California ESU) Chinook salmon Oncorhynchus C 1 1 tschawytscha INVERTEBRATES Bay checkerspot butterfly Euphydryas editha T I bayensis 1 PLANTS Tiburon paintbrush Castilleja aflnis spp. E neglecta I Coyote ceanothus Ceanothus ferrisae E - Santa Clara Valley dudleya Dudleya setchellii E I _. Metcalf Canyon jewelflower Streptanthus albidus E spp. albidus I California seablite Suaeda californica E L Mount Hamilton thistle Cirsiirm fontinale var. FSC I campylon E= Endangered, T= Threathened, C=Candidate, FSC=Federal Species of Special Concern 4 2 I I I Stream Maintenance Program Biological Assessment September 2001 I CONSULTATION TO DATE 8/29/01 USFWS (Ms. Cecilia Brown), SCVWD (Ms. Cindy Roessler, Mr. Doug Padley), and I consultants meet to discuss USFWS written comments on Draft Biological Assessment. 8/9/01 USFWS sends US. Army Corps of Engineers (USACE) written comments on Draft 1 Biological Assessment. 7/26/01 USFWS (Ms. Cecilia Brown and Dan Buford) and SCVWD meet to discuss progress and schedule for review of Draft Biological Assessment. I 7/2/01 USACE receives written comments from NMFS on Draft Biological Assessment. I 5/6/01 USACE requests consultation with NMFS and USFWS. 51710 1 USACE (Ms. Molly Martindale), USFWS (Ms. Cecilia Brown), NMFS (Ms. Maura II Eagan), SCVWD (Ms. Cindy Roessler, Mr. Ngoc Nguyen, Mr. Doug Padley), and consultants meet to discuss Draft Biological Assessment. I 4/18/01 USACE submits Draft Biological Assessment to USFWS and NMFS. 12/26/00 USWS (Mr. Ken Sanchez) sends list of Biological Opinions issued for Santa Clara I County (In response to 11/20/00 request by Mr. Jason Christie). 12/5/00 Ms. Cindy Roessler - Ms. Molly Martindale-U.S. Army Corps of Engineers (Corps) - I telephone conversation Corps can cover species.o utside of jurisdiction. (In response to 12/1/00 email request Corps include listed species outside of Corps jurisdiction). I 11/28/00 USFWS (Mr. Ken Sanchez - Ms. Karen Miller) letter to Mr. Doug Padley re Species List for Santa Clara County, in response to Mr. Doug Padley 11/17/00 request. I 11/27/00 Mr. Ken Sanchez phone call to Mr. Doug Padley indicating that USFWS will consider indir~ect. effects, especially urban development. 11/13/00 USFWS letter (Mr. Dale Pierce) to Ms. Cindy Roessler in response to Notice of Preparation 1 of DEIR (including list of species). 10/25/00 Ms. Cindy Roessler - Ms. Molly Martindale phone conversation re: Section 7 Consultation I under Clean Water Act. 2/10/00 District (Mr. Doug Padley, Mr. Jason Christie, and Ms. Cindy Roessler) meet with NMFS I to discuss Habitat Conservation Plan (HCP). District gives NMFS briefing book. 9/29/99 Mr. Doug Padley and Ms. Cindy Roessler meet with Mr. Curt McCasland from USFWS to 1 discuss HCP process and form. 5/25/99 District meets with USFWS to discuss HCP. I 3 I Stream Maintenance Program Biological Assessment September 2001 5/13/99 Mr. Doug Padley and Ms. Louisa Squires meet with USFWS (Mr. Dan Buford and Mr. Peter Bay) to discuss opportunities and constraints of mitigation at ponds A4 and A8. 2/2/99 Louisa Squires and Mr. Doug Padley meet with Mr. Ken Sanchez and Mr. Dan Buford of the USFWS and Ms. Molly Martindale of the USACE to discuss ponds A4-A8 multi-objective land use plan. 12/24/98 Mr. Jim Ferguson and Ms. Louisa Squires discuss mitigation at pond A8 with Mr. Mike Thabault. 11/17/98 Mr. Doug Padley letter to USFWS outlining scope of HCP, timeline and request for meeting. 11/4/98 Ms. Louisa Squires letter to Mr. Calvin Fong responding to letter from USFWS to Corps about use of Cargill Pond A-8. - 10/26/98 Letter from USFWS to Corps objecting to use of Cargill Pond A-8 for wetlands mitigation. 10/3/98 Ms. Louisa Squires discussion with USFWS (Mr. Ken Sanchez) on Pond A8. 91 15/98 Letter from Ms. Louisa Squires to Interagency participants describing field meeting on August 7, 1998 and August 26, 1998. 8/26/98 Interagency Field Meeting with USFWS (Mr. Dan Buford) Pond A8. 8/7/98 Interagency Field Meeting with Corps, U.S. Environmental Protection Agency (USEPA), USFWS (Ms. Janice Gann) Pond A8. 7/28/98 Mr. Doug Padley requests species list from USFWS to cover maintenance projects. 6/8/98 District Urgent Sediment Removal Project Compensatory Wetlands Mitigation and Monitoring Plan: Los Capitancillos Freshwater Migration Site andpond A8 Tidal Wetlands Mitigation Site. 9/19/97 Meeting with USFWS and CDFG to discuss Section 7 for Maintenance Program DEIR. 6/25/97 Mr. Doug Padley and Ms. Louisa Squires meet with USFWS; USFWS requests Wetland Plan before they will comment. 6/19/97 Submitted Preliminary Compensatory Wetlands Mitigation and Monitoring Plan. 5/14/97 Meeting with USFWS (Mr. Mike Thabault, Mr. Mike Westphal) to discuss USFWS position on ESA issues. 5/6/97 Mr. Doug Padley letter summarizing discussion with USFWS (Mr. Mike Westphal) on maintenance activities which could continue and those activities which needed review. 4