| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Abaya | Lake | native | 81251 |
| Agnébi | River (basin) | native | 272 |
| Albert | Lake | native | 78218 |
| Bandama | River (basin) | native | 57223 |
| Bani | River (basin) | native | 57223 |
| Benue | River (basin) | native | 57223 |
| Bia | River (basin) | native | 57223 |
| Blue Nile | River (basin) | native | 28714 |
| Boubo | River (basin) | native | 57223 |
| Chad | River (basin) | native | 57223 |
| Chari-Logone | River (basin) | native | 57223 |
| Comoé | River (basin) | native | 57223 |
| Corubal | River (basin) | native | 57223 |
| Cross | River (basin) | native | 81251 |
| Ébrié | Lagoon | native | 57223 |
| Ethiopian | Zoogeographic realm | endemic | 3202 |
| 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 | native | 57223 |
| Kogon | River (basin) | native | 57223 |
| Komadugu Yobe | River (basin) | native | 57223 |
| Kwa-Ibo | River (basin) | native | 57223 |
| Lower Niger | River (basin) | native | 57223 |
| Middle Niger | River (basin) | native | 57223 |
| Middle Nile | River (basin) | native | 28714 |
| Mono | River (basin) | native | 57223 |
| Niger | River (basin) | native | 57223 |
| Niger Delta | River (basin) | native | 57223 |
| Nile | River (basin) | native | 28714 |
| Northern East Rift Valley | Lake | native | 78218 |
| 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 |
| Turkana | Lake | native | 52331 |
| Upper Niger | River (basin) | native | 57223 |
| Victoria Nile | River (basin) | native | 4903 |
| Volta | River (basin) | native | 57223 |
| White Nile | River (basin) | native | 120561 |