| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Aruwimi | River (basin) | native | 122734 |
| Congo | River (basin) | endemic | 28136 |
| Ethiopian | Zoogeographic realm | endemic | 3509 |
| Itimbiri | River (basin) | native | 41590 |
| Léfini-Likouala | River (basin) | native | 83895 |
| Lindi-Tshopo | River (basin) | native | 122734 |
| Lower Congo | River (basin) | native | 42510 |
| Lualaba | River (basin) | native | 45616 |
| Middle Congo | River (basin) | native | 42480 |
| Ruki | River (basin) | native | 93897 |
| Ubangui | River (basin) | native | 45441 |
| Uélé | River (basin) | native | 42480 |
| Wagenia Falls | River (basin) | native | 45434 |