| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Aruwimi | River (basin) | native | 106290 |
| Congo | River (basin) | endemic | 96324 |
| Ethiopian | Zoogeographic realm | endemic | 7094 |
| Itimbiri | River (basin) | native | 106290 |
| Kasai | River (basin) | native | 11970 |
| Kwango | River (basin) | native | 96324 |
| Léfini-Likouala | River (basin) | native | 88782 |
| Lindi-Tshopo | River (basin) | native | 106290 |
| Lomami | River (basin) | native | 96324 |
| Lower Congo | River (basin) | native | 42510 |
| Lualaba | River (basin) | native | 45434 |
| Lukenie | River (basin) | native | 96324 |
| Marine Lower Congo | River (basin) | native | 96324 |
| Middle Congo | River (basin) | native | 41590 |
| Mongala | River (basin) | native | 96324 |
| Pool Malebo | Lake | native | 44985 |
| Ruki | River (basin) | native | 93897 |
| Sangha | River (basin) | native | 44840 |
| Sankuru | River (basin) | native | 13455 |
| Tanganyika | Lake | questionable | 6770 |
| Tumba | Lake | native | 96324 |
| Ubangui | River (basin) | native | 44840 |
| Uélé | River (basin) | native | 82705 |
| Upper Lualaba | River (basin) | native | 45434 |
| Wagenia Falls | River (basin) | native | 106245 |