| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Agnébi | River (basin) | native | 272 |
| Bandama | River (basin) | native | 103267 |
| Benue | River (basin) | native | 81263 |
| Boubo | River (basin) | native | 272 |
| Chad | River (basin) | native | 81263 |
| Comoé | River (basin) | native | 81263 |
| Ébrié | Lagoon | native | 101082 |
| Ethiopian | Zoogeographic realm | endemic | 3188 |
| Géba | River (basin) | native | 13331 |
| Kainji | Lake | native | 3034 |
| Niger | River (basin) | native | 81263 |
| Nile | River (basin) | native | 28714 |
| Ouémé | River (basin) | native | 81263 |
| Sassandra | River (basin) | native | 2835 |
| Volta | River (basin) | native | 81263 |