| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Aruwimi | River (basin) | native | 106290 |
| Bomu | River (basin) | native | 79650 |
| Chad | River (basin) | native | 81282 |
| Congo | River (basin) | native | 79650 |
| Ethiopian | Zoogeographic realm | endemic | 2940 |
| Itimbiri | River (basin) | native | 106290 |
| Kasai | River (basin) | native | 79650 |
| Kwilu | River (basin) | native | 114247 |
| Lindi-Tshopo | River (basin) | native | 106290 |
| Lower Congo | River (basin) | native | 79650 |
| Lualaba | River (basin) | native | 45434 |
| Middle Congo | River (basin) | native | 79650 |
| Pool Malebo | Lake | native | 41585 |
| Sangha | River (basin) | native | 79650 |
| Tanganyika | Lake | questionable | 93960 |
| Tumba | Lake | native | 41580 |
| Ubangui | River (basin) | native | 45441 |
| Uélé | River (basin) | native | 79650 |
| Upper Lualaba | River (basin) | native | 2970 |
| Victoria | Lake | error | 46152 |
| Wagenia Falls | River (basin) | native | 106245 |