| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Aruwimi | River (basin) | native | 248 |
| Banio | River (basin) | native | 81644 |
| Chad | River (basin) | native | 367 |
| Congo | River (basin) | native | 248 |
| Cross | River (basin) | native | 57129 |
| Ethiopian | Zoogeographic realm | endemic | 3820 |
| Itimbiri | River (basin) | native | 106290 |
| Kasai | River (basin) | native | 248 |
| Komo | River (basin) | native | 81644 |
| Kouilou-Niari | River (basin) | native | 81644 |
| Kwa-Ibo | River (basin) | native | 57129 |
| Kwango | River (basin) | native | 248 |
| Léfini-Likouala | River (basin) | native | 88782 |
| Lindi-Tshopo | River (basin) | native | 106290 |
| Loémé | River (basin) | native | 81644 |
| Lower Congo | River (basin) | native | 248 |
| Lualaba | River (basin) | native | 106245 |
| Lukenie | River (basin) | native | 127185 |
| Marine Lower Congo | River (basin) | native | 248 |
| Mbini | River (basin) | native | 81644 |
| Middle Congo | River (basin) | native | 248 |
| Mono | River (basin) | native | 57129 |
| Mungo | River (basin) | native | 81644 |
| Niger | River (basin) | native | 57129 |
| Niger Delta | River (basin) | native | 57129 |
| Ntem | River (basin) | native | 81644 |
| Nyanga | River (basin) | native | 81644 |
| Nyong | River (basin) | native | 81644 |
| Ogowe | River (basin) | native | 81644 |
| Ogun | River (basin) | native | 57129 |
| Oshun | River (basin) | native | 57129 |
| Ouémé | River (basin) | native | 13331 |
| Pool Malebo | Lake | native | 248 |
| Rio del Rey | River (basin) | native | 51193 |
| Ruki | River (basin) | native | 248 |
| Sanaga | River (basin) | native | 81644 |
| Sangha | River (basin) | native | 248 |
| Sankuru | River (basin) | native | 248 |
| Ubangui | River (basin) | native | 248 |
| Uélé | River (basin) | native | 248 |
| Volta | River (basin) | native | 57129 |
| Wagenia Falls | River (basin) | native | 248 |
| Wouri | River (basin) | native | 81644 |