| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Albert | Lake | native | 4903 |
| Congo | River (basin) | native | 36901 |
| Edward | Lake | native | 4903 |
| Ethiopian | Zoogeographic realm | endemic | 2801 |
| Kivu | Lake | questionable | 36901 |
| Lualaba | River (basin) | native | 93587 |
| Rusizi | River (basin) | native | 36901 |
| Sabaki | River (basin) | native | 30558 |
| Semliki | River (basin) | native | 4903 |
| Tana | River (basin) | native | 4967 |
| Tanganyika | Lake | native | 27628 |
| Turkana | Lake | native | 52331 |
| Victoria | Lake | native | 34290 |