| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Aruwimi | River (basin) | native | 106290 |
| Bangweulu | River (basin) | native | 1878 |
| Congo | River (basin) | native | 1878 |
| Ethiopian | Zoogeographic realm | endemic | 7094 |
| Kasai | River (basin) | native | 42034 |
| Kwango | River (basin) | native | 11970 |
| Lindi-Tshopo | River (basin) | native | 106290 |
| Lomami | River (basin) | native | 106245 |
| Lower Congo | River (basin) | native | 1878 |
| Lualaba | River (basin) | native | 45616 |
| Lukenie | River (basin) | native | 92931 |
| Malagarazi | River (basin) | native | 36901 |
| Middle Congo | River (basin) | native | 4910 |
| Mweru | Lake | native | 45616 |
| Pool Malebo | Lake | native | 1878 |
| Ruki | River (basin) | native | 41591 |
| Sangha | River (basin) | native | 51193 |
| Sankuru | River (basin) | native | 1880 |
| Ubangui | River (basin) | native | 45441 |
| Uélé | River (basin) | native | 1878 |
| Upper Lualaba | River (basin) | native | 45616 |
| Wagenia Falls | River (basin) | native | 106245 |