| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Aruwimi | River (basin) | native | 106290 |
| Bangweulu | River (basin) | native | 42135 |
| Congo | River (basin) | endemic | 45434 |
| Ethiopian | Zoogeographic realm | endemic | 4947 |
| Itimbiri | River (basin) | native | 106290 |
| Kasai | River (basin) | native | 46243 |
| Lindi-Tshopo | River (basin) | native | 106290 |
| Lower Congo | River (basin) | native | 42510 |
| Lualaba | River (basin) | native | 45616 |
| Marine Lower Congo | River (basin) | native | 41591 |
| Middle Congo | River (basin) | native | 41594 |
| Mweru | Lake | native | 246 |
| Pool Malebo | Lake | native | 41585 |
| Sangha | River (basin) | native | 46901 |
| Sankuru | River (basin) | native | 45626 |
| Tumba | Lake | native | 41580 |
| Ubangui | River (basin) | native | 45441 |
| Uélé | River (basin) | native | 41594 |
| Upper Lualaba | River (basin) | native | 2970 |
| Wagenia Falls | River (basin) | native | 106245 |