| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Albert | Lake | native | 82238 |
| Benue | River (basin) | questionable | 57223 |
| Chad | River (basin) | questionable | 57223 |
| Chari-Logone | River (basin) | questionable | 57223 |
| Edward | Lake | questionable | 82238 |
| Ethiopian | Zoogeographic realm | endemic | 3202 |
| Nile | River (basin) | native | 28714 |
| Shabeelle | River (basin) | native | 82238 |
| Turkana | Lake | native | 52331 |
| Victoria Nile | River (basin) | native | 4903 |
| White Nile | River (basin) | native | 120561 |