| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Albert | Lake | native | 4903 |
| Blue Nile | River (basin) | native | 28714 |
| Chad | River (basin) | native | 7094 |
| Ethiopian | Zoogeographic realm | endemic | 7094 |
| Middle Nile | River (basin) | native | 28714 |
| Nile | River (basin) | native | 28714 |
| Turkana | Lake | native | 28663 |
| Victoria Nile | River (basin) | native | 4903 |
| White Nile | River (basin) | native | 120561 |