| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Aruwimi | River (basin) | native | 106290 |
| Congo | River (basin) | endemic | 42480 |
| Ethiopian | Zoogeographic realm | endemic | 2801 |
| Itimbiri | River (basin) | native | 106290 |
| Kwango | River (basin) | native | 11970 |
| Kwilu | River (basin) | native | 11970 |
| Léfini-Likouala | River (basin) | native | 44840 |
| Lindi-Tshopo | River (basin) | questionable | 42480 |
| Lomami | River (basin) | native | 106245 |
| Lower Congo | River (basin) | native | 57537 |
| Marine Lower Congo | River (basin) | native | 113719 |
| Middle Congo | River (basin) | native | 4910 |
| Pool Malebo | Lake | native | 41585 |
| Ruki | River (basin) | native | 41580 |
| Sankuru | River (basin) | native | 11970 |
| Ubangui | River (basin) | native | 45441 |
| Wagenia Falls | River (basin) | native | 106245 |