| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Aruwimi | River (basin) | native | 106290 |
| Bangweulu | River (basin) | native | 52959 |
| Banio | River (basin) | native | 81639 |
| Congo | River (basin) | native | 27626 |
| Ethiopian | Zoogeographic realm | endemic | 2801 |
| Itimbiri | River (basin) | native | 106290 |
| Kasai | River (basin) | native | 11970 |
| Lindi-Tshopo | River (basin) | native | 106290 |
| Lomami | River (basin) | native | 106245 |
| Lower Congo | River (basin) | questionable | 246 |
| Lualaba | River (basin) | native | 45434 |
| Middle Congo | River (basin) | native | 46880 |
| Mweru | Lake | native | 52959 |
| Nyanga | River (basin) | native | 81639 |
| Ogowe | River (basin) | native | 81639 |
| Pool Malebo | Lake | native | 44985 |
| Sankuru | River (basin) | native | 11970 |
| Tanganyika | Lake | native | 41590 |
| Ubangui | River (basin) | native | 11970 |
| Uélé | River (basin) | native | 11970 |
| Upper Lualaba | River (basin) | native | 45434 |
| Wagenia Falls | River (basin) | native | 106245 |