| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Clear Lake | Lake | native | 86798 |
| Nearctic | Zoogeographic realm | endemic | 5723 |
| Pacific Coastal Complex | River (basin) | native | 81264 |
| Pajaro River | River (basin) | native | 86798 |
| Russian River | River (basin) | native | 86798 |
| Sacramento River | River (basin) | native | 86798 |
| Salinas River | River (basin) | native | 86798 |
| San Joaquin River | River (basin) | native | 86798 |