| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Aruwimi | River (basin) | native | 106290 |
| Benue | River (basin) | questionable | 42497 |
| Congo | River (basin) | native | 42493 |
| Ethiopian | Zoogeographic realm | endemic | 3203 |
| Itimbiri | River (basin) | native | 106290 |
| Kasai | River (basin) | native | 11970 |
| Léfini-Likouala | River (basin) | native | 44840 |
| Lindi-Tshopo | River (basin) | native | 106290 |
| Lower Congo | River (basin) | native | 45434 |
| Lualaba | River (basin) | native | 45434 |
| Malagarazi | River (basin) | native | 54847 |
| Marine Lower Congo | River (basin) | native | 1878 |
| Middle Congo | River (basin) | native | 41591 |
| Mweru | Lake | native | 1879 |
| Pool Malebo | Lake | native | 41585 |
| Sanaga | River (basin) | questionable | 51193 |
| Sangha | River (basin) | native | 46233 |
| Sankuru | River (basin) | native | 1880 |
| Tanganyika | Lake | native | 36899 |
| Tumba | Lake | native | 41580 |
| Ubangui | River (basin) | native | 45441 |
| Uélé | River (basin) | native | 41594 |
| Upper Lualaba | River (basin) | native | 45434 |
| Wagenia Falls | River (basin) | native | 106245 |