| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Aruwimi | River (basin) | native | 106290 |
| Bengo | River (basin) | native | 11970 |
| Chad | River (basin) | questionable | 83569 |
| Congo | River (basin) | native | 2970 |
| Cuanza | River (basin) | native | 11970 |
| Ethiopian | Zoogeographic realm | endemic | 2801 |
| Itimbiri | River (basin) | native | 106290 |
| Kasai | River (basin) | native | 11970 |
| Kwilu | River (basin) | native | 114247 |
| Lindi-Tshopo | River (basin) | native | 106290 |
| Lomami | River (basin) | native | 106245 |
| Lower Congo | River (basin) | native | 83564 |
| Lualaba | River (basin) | native | 36901 |
| Lukenie | River (basin) | native | 127185 |
| Middle Congo | River (basin) | native | 83564 |
| Okavango | River (basin) | native | 52193 |
| Pool Malebo | Lake | native | 41585 |
| Ruki | River (basin) | native | 93897 |
| Sangha | River (basin) | native | 51193 |
| Tanganyika | Lake | native | 36901 |
| Tumba | Lake | native | 41580 |
| Ubangui | River (basin) | native | 2988 |
| Uélé | River (basin) | native | 83564 |
| Upper Lualaba | River (basin) | native | 83564 |
| Upper Zambezi | River (basin) | native | 11970 |
| Wagenia Falls | River (basin) | native | 106245 |
| Zambezi | River (basin) | native | 52193 |