| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Agnébi | River (basin) | native | 272 |
| Albert | Lake | native | 4903 |
| Bandama | River (basin) | native | 57223 |
| Bani | River (basin) | native | 57223 |
| Benue River | River (basin) | native | 57223 |
| Bia | River (basin) | native | 57223 |
| Boubo | River (basin) | native | 57223 |
| Chari-Logone System | River (basin) | native | 57223 |
| Comoé | River (basin) | native | 57223 |
| Corubal | River (basin) | native | 57223 |
| Cross | River (basin) | native | 13331 |
| Ébrié Lagoon | Lagoon | native | 57223 |
| Ethiopian | Zoogeographic realm | endemic | 27886 |
| Fatala | River (basin) | native | 57223 |
| Gambia | River (basin) | native | 57223 |
| Géba | River (basin) | native | 57223 |
| Great Scarcies | River (basin) | questionable | 13331 |
| Inner Niger Delta | River (basin) | native | 57223 |
| Kainji Lake | Lake | native | 57223 |
| Kogon | River (basin) | native | 57223 |
| Komadugu Yobe | River (basin) | native | 57223 |
| Kwa-Ibo | River (basin) | native | 57223 |
| Lake Turkana | Lake | native | 52871 |
| 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 | 3202 |
| Ogun | River (basin) | native | 57223 |
| Ouémé | River (basin) | native | 57223 |
| Pra | River (basin) | native | 57223 |
| Sassandra | River (basin) | native | 57223 |
| Senegal | River (basin) | native | 57223 |
| Sio | River (basin) | native | 57223 |
| Sokoto | River (basin) | native | 57223 |
| Tano | River (basin) | native | 13331 |
| Upper Niger | River (basin) | native | 57223 |
| Victoria-Nile | River (basin) | native | 4903 |
| White Nile | River (basin) | native | 4903 |