| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Aruwimi | River (basin) | native | 41594 |
| Bangweulu | River (basin) | native | 45616 |
| Congo | River (basin) | endemic | 42019 |
| Ethiopian | Zoogeographic realm | endemic | 5331 |
| Itimbiri | River (basin) | native | 106290 |
| Kwilu | River (basin) | native | 80450 |
| Léfini-Likouala | River (basin) | native | 42019 |
| Lindi-Tshopo | River (basin) | native | 106290 |
| Lomami | River (basin) | native | 106245 |
| Lower Congo | River (basin) | native | 42510 |
| Lualaba | River (basin) | native | 42019 |
| Malagarazi | River (basin) | questionable | 45434 |
| Middle Congo | River (basin) | native | 42019 |
| Mweru | Lake | native | 46251 |
| Pool Malebo | Lake | native | 42019 |
| Ruki | River (basin) | native | 42019 |
| Sangha | River (basin) | native | 44840 |
| Sankuru | River (basin) | native | 46253 |
| Tumba | Lake | native | 1879 |
| Ubangui | River (basin) | native | 45441 |
| Uélé | River (basin) | native | 41594 |
| Upper Lualaba | River (basin) | native | 42019 |
| Wagenia Falls | River (basin) | native | 42480 |