| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Albert | Lake | native | 4903 |
| Benue | River (basin) | native | 81281 |
| Blue Nile | River (basin) | native | 28714 |
| Chad | River (basin) | native | 81281 |
| Cross | River (basin) | native | 81281 |
| Ethiopian | Zoogeographic realm | native | 7095 |
| Gambia | River (basin) | native | 81281 |
| Géba | River (basin) | native | 81281 |
| Kainji | Lake | native | 81281 |
| Middle Nile | River (basin) | native | 28714 |
| Niger | River (basin) | native | 81281 |
| Nile | River (basin) | native | 28714 |
| Ouémé | River (basin) | native | 28587 |
| Senegal | River (basin) | native | 81281 |
| Turkana | Lake | native | 52871 |
| Victoria Nile | River (basin) | native | 4903 |
| Volta | River (basin) | native | 81281 |
| White Nile | River (basin) | native | 120561 |