| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Aruwimi | River (basin) | native | 106290 |
| Bangweulu | River (basin) | native | 41590 |
| Congo | River (basin) | endemic | 78218 |
| Ethiopian | Zoogeographic realm | endemic | 3202 |
| Itimbiri | River (basin) | native | 42503 |
| Kasai | River (basin) | native | 11970 |
| Kwango | River (basin) | questionable | 12818 |
| Lindi-Tshopo | River (basin) | native | 106290 |
| Lower Congo | River (basin) | native | 42510 |
| Lualaba | River (basin) | native | 106245 |
| Middle Congo | River (basin) | native | 106245 |
| Mweru | Lake | native | 87966 |
| Sangha | River (basin) | native | 51193 |
| Ubangui | River (basin) | native | 45441 |
| Uélé | River (basin) | native | 41594 |
| Upper Lualaba | River (basin) | native | 2266 |
| Wagenia Falls | River (basin) | native | 106245 |