| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Aruwimi | River (basin) | native | 106290 |
| Congo | River (basin) | endemic | 85331 |
| Ethiopian | Zoogeographic realm | endemic | 3203 |
| Itimbiri | River (basin) | native | 106290 |
| Kasai | River (basin) | native | 11970 |
| Léfini-Likouala | River (basin) | native | 85331 |
| Lindi-Tshopo | River (basin) | native | 106290 |
| Lower Congo | River (basin) | native | 85331 |
| Lualaba | River (basin) | native | 45616 |
| Middle Congo | River (basin) | native | 4910 |
| Nyong | River (basin) | questionable | 81635 |
| Pool Malebo | Lake | native | 41585 |
| Ruki | River (basin) | native | 41580 |
| Sanaga | River (basin) | questionable | 87308 |
| Sangha | River (basin) | native | 85331 |
| Tumba | Lake | native | 41591 |
| Ubangui | River (basin) | native | 113655 |
| Uélé | River (basin) | native | 41590 |
| Upper Lualaba | River (basin) | native | 45616 |
| Wagenia Falls | River (basin) | native | 106245 |
| Wouri | River (basin) | questionable | 81635 |