| Écosystème | Type | Statut | Réf. |
|---|---|---|---|
| Aruwimi | River (basin) | native | 42032 |
| Benue | River (basin) | native | 81279 |
| Chad | River (basin) | native | 81279 |
| Congo | River (basin) | native | 42032 |
| Cross | River (basin) | native | 81279 |
| Ethiopian | Zoogeographic realm | endemic | 2880 |
| Itimbiri | River (basin) | native | 106290 |
| Kasai | River (basin) | native | 42032 |
| Léfini-Likouala | River (basin) | native | 44840 |
| Lindi-Tshopo | River (basin) | native | 106290 |
| Lomami | River (basin) | native | 42032 |
| Lower Congo | River (basin) | native | 42510 |
| Lualaba | River (basin) | native | 42032 |
| Mai-Ndombe | Lake | native | 1877 |
| Marine Lower Congo | River (basin) | native | 42032 |
| Middle Congo | River (basin) | native | 42032 |
| Mongala | River (basin) | native | 42032 |
| Mweru | Lake | native | 42032 |
| Niger | River (basin) | native | 81279 |
| Ntem | River (basin) | native | 80290 |
| Nyong | River (basin) | native | 80290 |
| Ogowe | River (basin) | native | 80290 |
| Pool Malebo | Lake | native | 42032 |
| Ruki | River (basin) | native | 93897 |
| Sangha | River (basin) | native | 42032 |
| Sankuru | River (basin) | native | 42032 |
| Tanganyika | Lake | questionable | 80290 |
| Tumba | Lake | native | 42032 |
| Ubangui | River (basin) | native | 45441 |
| Uélé | River (basin) | native | 42032 |
| Upper Lualaba | River (basin) | native | 42032 |
| Zambezi | River (basin) | native | 80290 |