| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Aruwimi | River (basin) | native | 41594 |
| Bangweulu | River (basin) | native | 95585 |
| Congo | River (basin) | native | 42019 |
| Ethiopian | Zoogeographic realm | endemic | 5331 |
| Itimbiri | River (basin) | native | 41590 |
| Kasai | River (basin) | native | 11970 |
| Kouilou-Niari | River (basin) | native | 92841 |
| Kwango | River (basin) | native | 11970 |
| Kwilu | River (basin) | native | 11970 |
| Léfini-Likouala | River (basin) | native | 88782 |
| Lindi-Tshopo | River (basin) | native | 106290 |
| Lomami | River (basin) | native | 106245 |
| Lualaba | River (basin) | native | 106245 |
| Mai-Ndombe | Lake | native | 1879 |
| Marine Lower Congo | River (basin) | native | 41594 |
| Middle Congo | River (basin) | native | 1879 |
| Mweru | Lake | native | 95585 |
| Ogowe | River (basin) | native | 92841 |
| Pool Malebo | Lake | native | 44985 |
| Ruki | River (basin) | native | 93897 |
| Tanganyika | Lake | native | 5331 |
| Tumba | Lake | native | 44912 |
| Ubangui | River (basin) | native | 45441 |
| Uélé | River (basin) | native | 41594 |
| Wagenia Falls | River (basin) | native | 106245 |