| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Aruwimi | River (basin) | native | 42032 |
| Chad | River (basin) | native | 83569 |
| Chari-Logone | River (basin) | native | 83569 |
| Congo | River (basin) | native | 59215 |
| Ethiopian | Zoogeographic realm | endemic | 5331 |
| Itimbiri | River (basin) | native | 42032 |
| Kasai | River (basin) | native | 42032 |
| Lindi-Tshopo | River (basin) | native | 42032 |
| Lomami | River (basin) | native | 42032 |
| Lower Congo | River (basin) | native | 42032 |
| Lualaba | River (basin) | native | 42032 |
| Lulonga | River (basin) | native | 42032 |
| Malagarazi | River (basin) | native | 98755 |
| Marine Lower Congo | River (basin) | native | 42032 |
| Middle Congo | River (basin) | native | 42032 |
| Pool Malebo | Lake | native | 42032 |
| Ruki | River (basin) | native | 42032 |
| Rusizi | River (basin) | native | 42032 |
| Sankuru | River (basin) | native | 42032 |
| Tanganyika | Lake | native | 42032 |
| Ubangui | River (basin) | native | 42032 |
| Uélé | River (basin) | native | 42032 |
| Upper Lualaba | River (basin) | native | 42032 |
| Wagenia Falls | River (basin) | native | 106245 |