DRAFT City of Santa Cruz Habitat Conservation Plan Conservation Strategy for Steelhead and Coho Salmon August 10, 2011 DRAFT HCP Fisheries Conservation Strategy Page 2 Table of Contents 1. Introduction ..................................................................................................................................... 9 2. Approach to the Conservation Strategy .................................................................................... 10 3. Biological Goals and Objectives .................................................................................................. 13 4. Avoidance and Minimization Measures ..................................................................................... 15 4.1. Water Supply Operations ...................................................................................................... 15 4.1.1. Water Diversions ............................................................................................................ 15 4.1.1.1. Minimizing the effects of City Diversions ............................................................. 16 4.1.1.2. Rationale for Developing Instream Flow Targets ............................................... 18 4.1.1.3. Liddell Spring Diversion .......................................................................................... 21 4.1.1.4. Reggiardo Creek Diversion .................................................................................... 24 4.1.1.5. Laguna Creek Diversion ......................................................................................... 24 4.1.1.6. Majors Creek Diversion .......................................................................................... 27 4.1.1.7. Newell Creek Diversion .......................................................................................... 30 4.1.1.8. San Lorenzo River Diversion at Felton ................................................................. 32 4.1.1.9. San Lorenzo River Diversion at Tait and San Lorenzo River Wells ................. 35 4.1.2. Reservoir Operations ...................................................................................................... 39 4.1.2.1. Chemical Algaecide Treatment of the Reservoir ................................................. 39 4.1.2.2. Testing Deluge and Gate Valves ........................................................................... 41 4.1.2.3. Woody Debris Removal on the Dam Face ........................................................... 41 4.2. Water System Operations and Maintenance ..................................................................... 42 4.2.1. Sediment Management .................................................................................................. 42 4.2.2. Fish Ladder and Screen Maintenance .......................................................................... 43 4.2.3. Pipeline Operations and Maintenance ......................................................................... 43 4.2.3.1. Conveyance Pipeline System Inspection and Repairs ....................................... 43 4.2.3.2. Finished Water Pipeline System Flushing and Repairs ...................................... 44 4.2.3.3. Pumping Well Return to San Lorenzo River ........................................................ 45 4.2.3.4. North Coast Valve Blow Off to San Lorenzo River ............................................. 45 4.3. Municipal Facility Operations and Maintenance ................................................................ 45 4.3.1. Flood Control Maintenance ........................................................................................... 45 4.3.1.1. Debris/Obstruction Removal .................................................................................. 46 4.3.1.2. Sediment Management/Removal .......................................................................... 46 4.3.1.3. Vegetation Management ........................................................................................ 47 4.3.2. Stormwater Maintenance .............................................................................................. 48 4.3.2.1. Best Management Practices .................................................................................. 48 4.3.2.2. Storm Drain Inspection and Cleaning .................................................................. 49 4.3.2.3. Structural Retrofits and Storm Drain Inlets and Basins .................................... 50 4.3.2.4. Sanitary Landfill Stormwater Management ......................................................... 51 4.3.3. Emergency Operations and Response ......................................................................... 52 4.3.4. Vegetation Management ............................................................................................... 52 4.4. Land Management ................................................................................................................. 53 4.4.1. Recreation ........................................................................................................................ 53 4.4.2. Facility Maintenance and Management ....................................................................... 53 DRAFT HCP Fisheries Conservation Strategy Page 3 4.4.2.1. Facility Repair .......................................................................................................... 53 4.4.2.2. Trail Maintenance and Management .................................................................... 53 4.4.2.3. Road Maintenance and Decommissioning ........................................................... 54 4.4.3. Habitat Management ...................................................................................................... 56 4.4.3.1. Aquatic Habitat Management ................................................................................ 56 4.4.3.2. Terrestrial Habitat Management ........................................................................... 57 4.5. Summary of Avoidance and Minimization Measures ........................................................ 57 5. Assessment of Impacts and Level of Take ................................................................................ 63 5.1. Steelhead .................................................................................................................................. 63 5.1.1. Water Diversions .............................................................................................................. 63 5.1.1.1. Steelhead Adult Migration ....................................................................................... 63 5.1.1.2. Steelhead Spawning and Incubation ..................................................................... 69 5.1.1.3. Steelhead Rearing .................................................................................................... 75 5.1.1.4. Steelhead Smolt Migration ...................................................................................... 86 5.1.1.5. Summary of Diversion Effects on Steelhead ........................................................ 90 5.1.2. Newell Large Woody Debris (LWD) .............................................................................. 90 5.1.3. Newell Sediment Transport ............................................................................................ 91 5.1.4. Flood Control Management ............................................................................................ 91 5.2. Coho Salmon ............................................................................................................................ 91 5.2.1. Water Diversions .............................................................................................................. 91 5.2.1.1. Coho Salmon Adult Migration ................................................................................. 92 5.2.1.2. Coho Salmon Spawning and Incubation ............................................................... 95 5.2.1.3. Coho Salmon Rearing .............................................................................................. 97 5.2.1.4. Coho Salmon Smolt Migration .............................................................................. 104 5.2.1.5. Summary of Diversion Effects on Coho Salmon ................................................ 104 5.2.2. Newell LWD .................................................................................................................... 105 5.2.3. Newell Sediment Transport .......................................................................................... 105 5.2.4. Flood Control Management .......................................................................................... 105 6. Mitigation Measures .................................................................................................................... 106 7. Monitoring and Adaptive Management .................................................................................... 111 7.1. Compliance Monitoring ........................................................................................................ 113 7.2. Goals and Objectives Monitoring ....................................................................................... 114 7.2.1. Steelhead and coho salmon population abundance................................................ 114 7.2.2. Steelhead and coho salmon habitat quality ............................................................. 115 7.3. Mitigation Effectiveness