| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Albert | Lake | native | 40587 |
| Congo | River (basin) | native | 3498 |
| Edward | Lake | native | 40587 |
| Ethiopian | Zoogeographic realm | endemic | 3498 |
| Lower Congo | River (basin) | native | 44796 |
| Lualaba | River (basin) | native | 40587 |
| Malagarazi | River (basin) | native | 54847 |
| Marine Lower Congo | River (basin) | native | 40587 |
| Middle Congo | River (basin) | native | 40587 |
| Middle Nile | River (basin) | native | 28714 |
| Nile | River (basin) | native | 28714 |
| Pool Malebo | Lake | native | 40587 |
| Rusizi | River (basin) | native | 98755 |
| Tanganyika | Lake | native | 3498 |
| Turkana | Lake | native | 52331 |
| Upper Lualaba | River (basin) | native | 40587 |
| Victoria | Lake | native | 3498 |
| Wagenia Falls | River (basin) | native | 40587 |
| White Nile | River (basin) | native | 120561 |