| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Aruwimi | River (basin) | native | 248 |
| Chad | River (basin) | questionable | 31256 |
| Congo | River (basin) | native | 248 |
| Cross | River (basin) | native | 57129 |
| Ethiopian | Zoogeographic realm | endemic | 3820 |
| Itimbiri | River (basin) | native | 248 |
| Kasai | River (basin) | native | 248 |
| Kienke | River (basin) | native | 81644 |
| Komo | River (basin) | native | 81644 |
| Kouilou-Niari | River (basin) | native | 92841 |
| Kwilu | River (basin) | native | 248 |
| Lindi-Tshopo | River (basin) | native | 106290 |
| Lomami | River (basin) | native | 248 |
| Lualaba | River (basin) | native | 106245 |
| Lukenie | River (basin) | native | 127185 |
| Marine Lower Congo | River (basin) | questionable | 88782 |
| Mbini | River (basin) | native | 81644 |
| Middle Congo | River (basin) | native | 248 |
| Muni | River (basin) | native | 81644 |
| Niger | River (basin) | native | 57129 |
| Niger Delta | River (basin) | native | 57129 |
| Ntem | River (basin) | native | 81644 |
| Nyong | River (basin) | native | 81644 |
| Ogowe | River (basin) | native | 81644 |
| Ouémé | River (basin) | questionable | 57129 |
| Ruki | River (basin) | native | 93897 |
| Sanaga | River (basin) | native | 248 |
| Sangha | River (basin) | native | 248 |
| Sankuru | River (basin) | native | 13455 |
| Ubangui | River (basin) | native | 248 |
| Wagenia Falls | River (basin) | native | 106245 |