| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Aruwimi | River (basin) | native | 106290 |
| Bomu | River (basin) | native | 52248 |
| Congo | River (basin) | endemic | 52248 |
| Ethiopian | Zoogeographic realm | endemic | 5654 |
| Itimbiri | River (basin) | native | 106290 |
| Kotto | River (basin) | native | 52248 |
| Lindi-Tshopo | River (basin) | native | 106290 |
| Lomami | River (basin) | native | 106245 |
| Lualaba | River (basin) | native | 52248 |
| Middle Congo | River (basin) | native | 52248 |
| Mongala | River (basin) | native | 52248 |
| Ruki | River (basin) | native | 52248 |
| Ubangui | River (basin) | native | 52248 |
| Uélé | River (basin) | native | 52248 |
| Upper Lualaba | River (basin) | native | 52248 |
| Wagenia Falls | River (basin) | native | 106245 |