| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Agnébi | River (basin) | native | 81279 |
| Albert | Lake | native | 42019 |
| Bandama | River (basin) | native | 81279 |
| Benue River | River (basin) | native | 81279 |
| Bia | River (basin) | native | 81279 |
| Blue Nile | River (basin) | native | 28714 |
| Casamance | River (basin) | native | 81279 |
| Cavally | River (basin) | native | 81279 |
| Chari-Logone System | River (basin) | native | 81279 |
| Comoé | River (basin) | native | 81279 |
| Corubal | River (basin) | native | 81279 |
| Cross | River (basin) | native | 80290 |
| Ébrié Lagoon | Lagoon | native | 81279 |
| Ethiopian | Zoogeographic realm | endemic | 2880 |
| Gambia | River (basin) | native | 81279 |
| Géba | River (basin) | native | 81279 |
| Kainji Lake | Lake | native | 81279 |
| Konkouré | River (basin) | native | 81279 |
| Lake Turkana | Lake | native | 52331 |
| Mono | River (basin) | native | 81279 |
| Niger | River (basin) | native | 81279 |
| Niger Delta | River (basin) | native | 81279 |
| Nile | River (basin) | native | 80290 |
| Ogun | River (basin) | native | 81279 |
| Ouémé | River (basin) | native | 81279 |
| Pra | River (basin) | native | 81279 |
| Rio del Rey | River (basin) | native | 80290 |
| Saint Paul | River (basin) | native | 13331 |
| San Pedro | River (basin) | native | 81279 |
| Sassandra | River (basin) | native | 81279 |
| Senegal | River (basin) | native | 81279 |
| Victoria | Lake | misidentification | 41374 |
| White Nile | River (basin) | native | 58460 |