| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Edward | Lake | misidentification | 248 |
| Ethiopian | Zoogeographic realm | endemic | 3820 |
| Malagarazi | River (basin) | native | 54847 |
| Nile | River (basin) | native | 28714 |
| Rusizi | River (basin) | native | 98755 |
| Tanganyika | Lake | native | 78218 |
| Victoria | Lake | native | 78218 |
| Victoria Nile | River (basin) | native | 248 |
| White Nile | River (basin) | native | 120561 |