| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Aruwimi River | River (basin) | native | 106290 |
| Congo | River (basin) | endemic | 51193 |
| Ethiopian | Zoogeographic realm | endemic | 26190 |
| Itimbiri River | River (basin) | native | 106290 |
| Kasai River | River (basin) | native | 26190 |
| Kwango River | River (basin) | native | 1878 |
| Kwango River | River (basin) | native | 1878 |
| Léfini-Likouala Region | River (basin) | native | 88782 |
| Lindi-Tshopo Region | River (basin) | native | 106290 |
| Lower Congo | River (basin) | native | 26190 |
| Lualaba | River (basin) | native | 26190 |
| Lulonga | River (basin) | native | 26190 |
| Malebo Pool | Lake | native | 26190 |
| Marine Lower Congo | River (basin) | native | 26190 |
| Middle Congo | River (basin) | native | 26190 |
| Sangha | River (basin) | native | 51193 |
| Sankuru | River (basin) | native | 26190 |
| Tanganyika | Lake | misidentification | 1440 |
| Ubangui | River (basin) | native | 26190 |
| Uélé | River (basin) | native | 26190 |
| Upper Lualaba | River (basin) | native | 26190 |
| Wagenia Falls | River (basin) | native | 106245 |