| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Aruwimi | River (basin) | native | 106290 |
| Chiloango | River (basin) | native | 81650 |
| Congo | River (basin) | native | 81650 |
| Ethiopian | Zoogeographic realm | endemic | 6803 |
| Lukenie | River (basin) | native | 127185 |
| Mai-Ndombe | Lake | native | 41590 |
| Middle Congo | River (basin) | native | 106245 |
| Nyong | River (basin) | questionable | 81650 |
| Pool Malebo | Lake | native | 39599 |
| Ruki | River (basin) | native | 93897 |
| Ubangui | River (basin) | native | 45441 |