| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Aruwimi | River (basin) | native | 106290 |
| Bangweulu | River (basin) | native | 95585 |
| Congo | River (basin) | endemic | 41590 |
| Ethiopian | Zoogeographic realm | endemic | 5331 |
| Itimbiri | River (basin) | native | 106290 |
| Kwango | River (basin) | native | 74421 |
| Léfini-Likouala | River (basin) | native | 74421 |
| Lindi-Tshopo | River (basin) | native | 106290 |
| Lomami | River (basin) | native | 106245 |
| Lower Congo | River (basin) | native | 74421 |
| Lualaba | River (basin) | native | 36901 |
| Lukenie | River (basin) | native | 74421 |
| Malagarazi | River (basin) | questionable | 36901 |
| Middle Congo | River (basin) | native | 41590 |
| Mongala | River (basin) | native | 41590 |
| Mweru | Lake | native | 41590 |
| Ogowe | River (basin) | questionable | 52343 |
| Pool Malebo | Lake | native | 97590 |
| Ruki | River (basin) | native | 74421 |
| Tanganyika | Lake | questionable | 4967 |
| Ubangui | River (basin) | native | 41590 |
| Upper Lualaba | River (basin) | native | 45434 |
| Wagenia Falls | River (basin) | native | 106245 |