| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Bandama | River (basin) | native | 86396 |
| Benue | River (basin) | native | 86396 |
| Bia | River (basin) | native | 86396 |
| Blue Nile | River (basin) | native | 28714 |
| Chad | River (basin) | native | 86396 |
| Comoé | River (basin) | native | 86396 |
| Cross | River (basin) | native | 81638 |
| Ébrié | Lagoon | native | 28587 |
| Ethiopian | Zoogeographic realm | endemic | 7094 |
| Gambia | River (basin) | native | 86396 |
| Géba | River (basin) | native | 86396 |
| Kainji | Lake | native | 86396 |
| Middle Nile | River (basin) | native | 28714 |
| Mono | River (basin) | native | 86396 |
| Niger | River (basin) | native | 86396 |
| Nile | River (basin) | native | 28714 |
| Ogun | River (basin) | native | 86396 |
| Ouémé | River (basin) | native | 86396 |
| Sassandra | River (basin) | native | 86396 |
| Senegal | River (basin) | native | 86396 |
| Tano | River (basin) | native | 30488 |
| Volta | River (basin) | native | 86396 |
| White Nile | River (basin) | native | 120561 |