STATE OF CALIFORNIA STATE WATER RESOURCES CONTROL BOARD In the Matter of Water Quality Certification for TURLOCK IRRIGATION DISTRICT AND MODESTO IRRIGATION DISTRICT DON PEDRO HYDROELECTRIC PROJECT AND LA GRANGE HYDROELECTRIC PROJECT FEDERAL ENERGY REGULATORY COMMISSION PROJECT NOS. 2299 AND 14581 Sources: Tuolumne River and Tributaries Counties: Stanislaus and Tuolumne WATER QUALITY CERTIFICATION FOR FEDERAL PERMIT OR LICENSE Don Pedro Hydroelectric Project and La Grange Hydroelectric Project January 2021 Final Water Quality Certification Table of Contents 1.0 Projects Background ......................................................................................... 7 2.0 Projects Description ........................................................................................... 8 3.0 Water Rights ....................................................................................................... 8 4.0 Federal Energy Regulatory Commission Licensing Process ....................... 13 5.0 Regulatory Authority ........................................................................................ 13 5.1 Water Quality Certification and Related Authorities ..................................... 13 5.2 Water Quality Control Plans and Related Authorities ................................... 14 5.3 Clean Water Act Section 303(d) Listing .......................................................... 16 5.4 Construction General Permit ........................................................................... 16 5.5 State Wetland Definition and Procedures for Discharges of Dredged or Fill Material to Waters of the State ........................................................................ 17 5.6 Aquatic Weed Control General Permit ............................................................ 17 5.7 Statewide Mercury Provisions ......................................................................... 17 6.0 California Environmental Quality Act ............................................................. 18 7.0 Rationale for Water Quality Certification Conditions .................................... 18 7.1 Rationale for Condition 1 –Instream Flows .................................................... 19 7.2 Rationale for Condition 2 – Ramping Rates ................................................... 28 7.3 Rationale for Condition 3 – Temperature Management and Monitoring Plan ........................................................................................................................... 29 7.4 Rationale for Condition 4 – Extremely Dry Conditions ................................. 33 7.5 Rationale for Condition 5 – Southern Delta Salinity ...................................... 33 7.6 Rationale for Condition 6 – Tuolumne River and Regional Watershed Management Coordination .............................................................................. 34 7.7 Rationale for Condition 7 – Annual Review Meeting ..................................... 35 7.8 Rationale for Condition 8 – Water Quality Monitoring and Management .... 35 7.9 Rationale for Condition 9 – Large Woody Material Management ................. 36 7.10 Rationale for Condition 10 – Erosion and Sediment Management .............. 37 7.11 Rationale for Condition 11 – Gravel Augmentation ....................................... 38 7.12 Rationale for Condition 12 – Riparian, Spawning, and Floodplain Management ...................................................................................................... 38 7.13 Rationale for Condition 13 – Predator Suppression Plan ............................. 40 7.14 Rationale for Condition 14 – Aquatic Invasive Species Management ......... 40 7.15 Rationale for Condition 15 – Recreation Facilities Management ................. 40 7.16 Rationale for Condition 16 – Road Management ........................................... 41 ii Don Pedro Hydroelectric Project and La Grange Hydroelectric Project January 2021 Final Water Quality Certification 7.17 Rationale for Condition 17 – Biological Resources Management ................ 41 7.18 Rationale for Condition 18 – Comprehensive Monitoring, Assessment, Reporting, and Special Studies ....................................................................... 42 7.19 Rationale for Condition 19 – Construction and Maintenance ....................... 43 7.20 Rationale for Condition 20 – Reintroduction of Anadromous Fish .............. 43 7.21 Rationale for Conditions 21 through 45.......................................................... 44 8.0 Conclusion ........................................................................................................ 44 9.0 Water Quality Certification Conditions ........................................................... 45 Instream Flows ................................................................................ 45 Water Year Types ............................................................................................. 45 Minimum Instream Flows Below La Grange Dam and Below One or More Potential Points of Diversion or Rediversion ............................... 47 Pulse Flows ....................................................................................................... 48 Bay-Delta Plan Flow Objectives ...................................................................... 50 Compliance Methods ....................................................................................... 50 1.E.1 Minimum Instream Flows ................................................................................. 52 1.E.2 Pulse Flows ....................................................................................................... 53 1.E.3 LSJR Flow Objectives ...................................................................................... 53 1.E.4 Unplanned Temporary Flow Modifications .................................................... 53 Annual Operations Plan ................................................................................... 54 Dry Year Management Operations Plan ......................................................... 56 Ramping Rates ................................................................................ 56 Temperature Management and Monitoring Plan .......................... 57 Extremely Dry Conditions .............................................................. 61 Southern Delta Salinity Objective .................................................. 62 Tuolumne River and Regional Watershed Management Coordination .................................................................................... 62 Annual Review Meeting .................................................................. 64 Water Quality Monitoring and Management ................................. 65 Large Woody Material Management .............................................. 69 Erosion and Sediment Management ............................................. 71 Gravel Augmentation and Management ........................................ 72 Riparian, Spawning, and Floodplain Management ....................... 74 Predator Suppression Plan ............................................................ 78 Aquatic Invasive Species Management Plan ................................ 79 iii Don Pedro Hydroelectric Project and La Grange Hydroelectric Project January 2021 Final Water Quality Certification Recreation Facilities Management ................................................ 80 Road Management .......................................................................... 81 Biological Resources Management ............................................... 82 Monitoring, Assessment, Reporting, and Special Studies .......... 85 Construction and Maintenance ...................................................... 89 Reintroduction of Anadromous Fish ............................................. 90 CONDITIONS 21 – 45 ................................................................................................... 91 List of Tables Table A. Water Rights Held by TID and MID for the Projects. ................................ 12 Table 1. Minimum Instream Flow Requirements downstream of La Grange Dam, River Mile 51.7 (cubic feet per second) ................................................ 47 Table 2. Minimum Instream Flow Requirements Downstream of Potential New Point or Points of Diversion or Rediversion near River Mile 25.9 (cubic feet per second) .......................................................................... 48 Table 3. Tuolumne River Temperature Targets ....................................................... 58 Table 4. Tuolumne River Dissolved Oxygen Water Quality Objectives ................. 66 List of Figures Figure 1. General Map of San Joaquin River Basin Showing Locations of Don Pedro and La Grange Hydroelectric Projects ........................................ 9 Figure 2. Don Pedro and La Grange Hydroelectric Projects Site Location Map ................................................................................................................. 10 Figure 3. 2018 SED Appendix F.1, page F.1-210. “Figure F.1.6-6a Effects of New Don Pedro Storage on New Don Pedro and La Grange Simulated Water Temperatures September – December for Baseline Conditions 1970 – 2003.” .......................................................................................... 32 List of Attachments Attachment A: Detailed Projects Description Attachment B: Consolidated Instream Flow Requirements iv Don Pedro Hydroelectric Project and La Grange Hydroelectric