| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Aruwimi River | River (basin) | native | 106290 |
| Benue River | River (basin) | native | 13331 |
| Chari-Logone System | River (basin) | native | 114071 |
| Congo | River (basin) | native | 3203 |
| Cross | River (basin) | native | 2915 |
| Cuanza | River (basin) | native | 99599 |
| Ethiopian | Zoogeographic realm | endemic | 3203 |
| Itimbiri River | River (basin) | native | 106290 |
| Kasai River | River (basin) | native | 114071 |
| Kivu | Lake | questionable | 51936 |
| Lindi-Tshopo Region | River (basin) | native | 106290 |
| Lualaba | River (basin) | native | 41590 |
| Malebo Pool | Lake | native | 41585 |
| Marine Lower Congo | River (basin) | native | 1879 |
| Middle Congo | River (basin) | native | 4910 |
| Mweru | Lake | native | 246 |
| Niger | River (basin) | native | 3203 |
| Ogun | River (basin) | native | 2915 |
| Ruki River Region | River (basin) | native | 93897 |
| Sanaga | River (basin) | native | 114071 |
| Sangha | River (basin) | native | 46233 |
| Sankuru | River (basin) | native | 1880 |
| Tanganyika | Lake | native | 114071 |
| Tumba | Lake | native | 41580 |
| Ubangui | River (basin) | native | 45441 |
| Uélé | River (basin) | native | 41594 |
| Upper Lualaba | River (basin) | native | 45616 |
| Wagenia Falls | River (basin) | native | 106245 |
| Wouri | River (basin) | native | 114071 |