| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Aruwimi | River (basin) | native | 106290 |
| Benue | River (basin) | questionable | 83752 |
| Chad | River (basin) | questionable | 83360 |
| Chari-Logone | River (basin) | questionable | 3047 |
| Congo | River (basin) | endemic | 83752 |
| Ethiopian | Zoogeographic realm | endemic | 3203 |
| Kasai | River (basin) | native | 83752 |
| Lindi-Tshopo | River (basin) | native | 106290 |
| Lower Congo | River (basin) | native | 83752 |
| Lualaba | River (basin) | native | 83752 |
| Marine Lower Congo | River (basin) | native | 83752 |
| Middle Congo | River (basin) | native | 83752 |
| Mongala | River (basin) | native | 83752 |
| Pool Malebo | Lake | native | 44985 |
| Ruki | River (basin) | native | 83752 |
| Sankuru | River (basin) | native | 46253 |
| Tumba | Lake | native | 83752 |
| Ubangui | River (basin) | native | 83752 |
| Uélé | River (basin) | native | 83752 |
| Upper Lualaba | River (basin) | native | 83752 |
| Wagenia Falls | River (basin) | native | 83752 |