| San Pablo Reservoir | CA | Lake/Reservoir/Pond | Not Supporting | 6 | 785 |
| San Vicente Reservoir | CA | Lake/Reservoir/Pond | Not Supporting | 5 | 1,088 |
| Sand Canyon Reservoir (Orange County) | CA | Lake/Reservoir/Pond | Not Supporting | 1 | 24 |
| Santa Fe Dam Park Lake | CA | Lake/Reservoir/Pond | Not Supporting | 1 | 19 |
| Santa Rosa Hydrologic Subarea, Spring Lake (Santa Rosa Creek Reservoir) | CA | Lake/Reservoir/Pond | Not Supporting | 1 | 72 |
| Schwan Lake | CA | Lake/Reservoir/Pond | Not Supporting | 4 | 23 |
| Scotts Flat Reservoir | CA | Lake/Reservoir/Pond | Not Supporting | 1 | 661 |
| Shadow Cliffs Reservoir | CA | Lake/Reservoir/Pond | Not Supporting | 2 | 143 |
| Shasta Lake (area where West Squaw Creek enters) | CA | Lake/Reservoir/Pond | Not Supporting | 3 | 34 |
| Silverwood Lake | CA | Lake/Reservoir/Pond | Not Supporting | 6 | 906 |
| Siphon Reservoir (Orange County) | CA | Lake/Reservoir/Pond | Not Supporting | 1 | 24 |
| Siskiyou, Lake | CA | Lake/Reservoir/Pond | Not Supporting | 1 | 434 |
| Skinner Lake | CA | Lake/Reservoir/Pond | Not Supporting | 1 | 996 |
| Slab Creek Reservoir (El Dorado County) | CA | Lake/Reservoir/Pond | Not Supporting | 1 | 242 |
| Soda Lake | CA | Lake, Saline | Not Supporting | 1 | 2,541 |
| Solano Lake | CA | Lake/Reservoir/Pond | Not Supporting | 1 | 25 |
| Soulajule Reservoir | CA | Lake/Reservoir/Pond | Not Supporting | 1 | 49 |
| Spaulding, Lake | CA | Lake/Reservoir/Pond | Not Supporting | 1 | 694 |
| Stevens Creek Reservoir | CA | Lake/Reservoir/Pond | Not Supporting | 4 | 83 |
| Stony Gorge Reservoir | CA | Lake/Reservoir/Pond | Not Supporting | 1 | 1,383 |
| Success Lake | CA | Lake/Reservoir/Pond | Not Supporting | 2 | 2,471 |
| Sunbeam Lake | CA | Lake/Reservoir/Pond | Not Supporting | 2 | 9.67 |
| Sutherland Reservoir | CA | Lake/Reservoir/Pond | Not Supporting | 7 | 556 |
| Sweetwater Reservoir | CA | Lake/Reservoir/Pond | Not Supporting | 2 | 1,310 |
| Tahoe Keys Sailing Lagoon | CA | Lake/Reservoir/Pond | Not Supporting | 1 | 113 |
| Tahoe, Lake | CA | Lake/Reservoir/Pond | Not Supporting | 2 | 84,092 |
| Thermalito Afterbay | CA | Lake/Reservoir/Pond | Not Supporting | 1 | 4,037 |
| Thermalito Diversion Pool | CA | Lake/Reservoir/Pond | Fully Supporting | 0 | 298 |
| Thermalito Forebay | CA | Lake/Reservoir/Pond | Not Supporting | 1 | 563 |
| Topaz Lake | CA | Lake/Reservoir/Pond | Not Supporting | 1 | 921 |
| Trinity Lake (was Claire Engle Lake) | CA | Lake/Reservoir/Pond | Not Supporting | 1 | 15,587 |
| Tulloch Reservoir | CA | Lake/Reservoir/Pond | Not Supporting | 1 | 939 |
| Turlock Lake | CA | Lake/Reservoir/Pond | Not Supporting | 1 | 2,824 |
| Twin Lake, Upper (East Walker River HU) | CA | Lake/Reservoir/Pond | Not Supporting | 1 | 306 |
| Upper San Leandro Reservoir | CA | Lake/Reservoir/Pond | Not Supporting | 1 | 758 |
| Vasona Lake | CA | Lake/Reservoir/Pond | Not Supporting | 3 | 52 |
| Webb, Lake | CA | Lake/Reservoir/Pond | Not Supporting | 1 | 864 |
| West Valley Reservoir | CA | Lake/Reservoir/Pond | Not Supporting | 1 | 996 |
| Whiskeytown Lake (areas near Oak Bottom, Brandy Creek Campgrounds and Whiskeytown) | CA | Lake/Reservoir/Pond | Not Supporting | 1 | 170 |
| Wiest Lake | CA | Lake/Reservoir/Pond | Not Supporting | 3 | 48 |
| Wildlife Lake | CA | Lake/Reservoir/Pond | Not Supporting | 1 | 14 |
| Wildwood, Lake (Nevada County) | CA | Lake/Reservoir/Pond | Not Supporting | 1 | 289 |
| William Pond (Sacramento County) | CA | Lake/Reservoir/Pond | Not Supporting | 1 | 33 |
| Woodward Reservoir | CA | Lake/Reservoir/Pond | Not Supporting | 1 | 1,717 |
| Zayak (Swan) Lake | CA | Lake/Reservoir/Pond | Not Supporting | 1 | 24 |