| Arrowhead Marsh | Alameda, CA | 2.4 miles | SE |
| George Whittell Marsh | Contra Costa, CA | 17.4 miles | NW |
| Shorebird Marsh | Marin, CA | 19.4 miles | NW |
| Hidden Lake | Marin, CA | 24.4 miles | NW |
| Mountain View Tidal Marsh | Santa Clara, CA | 25 miles | SE |
| Crittenden Marsh | Santa Clara, CA | 25.2 miles | SE |
| Stevens Creek Tidal Marsh | Santa Clara, CA | 25.3 miles | SE |
| Appleby Bay | Napa, CA | 29.3 miles | NW |
| Fly Bay | Napa, CA | 30.1 miles | NW |
| Little Franks Tract | Contra Costa, CA | 36 miles | NE |
| Short Slough (historical) | Contra Costa, CA | 37.4 miles | NE |
| Olema Marsh | Marin, CA | 37.6 miles | NW |
| Fishermans Slough (historical) | Contra Costa, CA | 37.8 miles | NE |
| Marshall Marsh | Marin, CA | 45.4 miles | NW |
| Livermore Marsh | Marin, CA | 46 miles | NW |
| Beaver Lake | Sacramento, CA | 48 miles | NE |
| Ledson Marsh | Sonoma, CA | 48.2 miles | NW |
| Scott Creek Marsh | Santa Cruz, CA | 51.2 miles | SW |
| Arana Marsh | Santa Cruz, CA | 56.9 miles | SE |
| Nearys Lagoon | Santa Cruz, CA | 57.4 miles | SE |
| Valencia Lagoon | Santa Cruz, CA | 58.8 miles | SE |
| Anderson Marsh | Lake, CA | 82.3 miles | NW |
| Laguna Seca | Monterey, CA | 86.6 miles | SE |
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