| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Albert | Lake | native | 34290 |
| Blue Nile | River (basin) | native | 28714 |
| Edward | Lake | native | 34290 |
| Ethiopian | Zoogeographic realm | endemic | 3203 |
| Lower Nile | River (basin) | native | 1878 |
| Middle Nile | River (basin) | native | 28714 |
| Nile | River (basin) | native | 28714 |
| Shabeelle | River (basin) | native | 52331 |
| Tana | River (basin) | questionable | 52331 |
| Turkana | Lake | native | 52331 |
| Victoria | Lake | native | 34290 |
| Victoria Nile | River (basin) | native | 34290 |
| White Nile | River (basin) | native | 120561 |