| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Bandama | River (basin) | native | 81282 |
| Benue | River (basin) | native | 13331 |
| Chad | River (basin) | native | 81282 |
| Comoé | River (basin) | native | 81282 |
| Cross | River (basin) | native | 81282 |
| Ethiopian | Zoogeographic realm | endemic | 2940 |
| Géba | River (basin) | native | 13331 |
| Middle Nile | River (basin) | native | 28714 |
| Niger | River (basin) | native | 81282 |
| Nile | River (basin) | native | 2940 |
| Ouémé | River (basin) | native | 13331 |
| Turkana | Lake | native | 52871 |
| Volta | River (basin) | native | 81282 |
| White Nile | River (basin) | native | 28714 |