| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Bani | River (basin) | native | 57223 |
| Benue | River (basin) | native | 57223 |
| Casamance | River (basin) | native | 57223 |
| Chad | River (basin) | native | 57223 |
| Chari-Logone | River (basin) | native | 57223 |
| Congo | River (basin) | native | 41414 |
| Cross | River (basin) | native | 81251 |
| Ethiopian | Zoogeographic realm | endemic | 3202 |
| Gambia | River (basin) | native | 57223 |
| Géba | River (basin) | native | 57223 |
| Great Scarcies | River (basin) | questionable | 81251 |
| Inner Niger Delta | River (basin) | native | 57223 |
| Komadugu Yobe | River (basin) | native | 57223 |
| Kotto | River (basin) | native | 41414 |
| Kwa-Ibo | River (basin) | native | 57223 |
| Lower Niger | River (basin) | native | 57223 |
| Middle Niger | River (basin) | native | 57223 |
| Mono | River (basin) | native | 57223 |
| Niger | River (basin) | native | 57223 |
| Niger Delta | River (basin) | native | 57223 |
| Nile | River (basin) | native | 28714 |
| Ntem | River (basin) | native | 81251 |
| Ogun | River (basin) | native | 13331 |
| Ouémé | River (basin) | native | 57223 |
| Senegal | River (basin) | native | 57223 |
| Sio | River (basin) | native | 57223 |
| Sokoto | River (basin) | native | 57223 |
| Upper Niger | River (basin) | native | 57223 |
| Volta | River (basin) | native | 57223 |
| White Nile | River (basin) | native | 120561 |