| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Albert | Lake | native | 4903 |
| Benue | River (basin) | native | 81279 |
| Blue Nile | River (basin) | native | 28714 |
| Chad | River (basin) | native | 81279 |
| Ethiopian | Zoogeographic realm | endemic | 5331 |
| Gambia | River (basin) | native | 81279 |
| Kainji | Lake | native | 28265 |
| Middle Nile | River (basin) | native | 28714 |
| Niger | River (basin) | native | 81279 |
| Nile | River (basin) | native | 28714 |
| Sanaga | River (basin) | native | 51193 |
| Senegal | River (basin) | native | 81279 |
| Turkana | Lake | native | 52331 |
| Volta | River (basin) | native | 81279 |
| White Nile | River (basin) | native | 120561 |