| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Aruwimi | River (basin) | native | 106290 |
| Congo | River (basin) | endemic | 3570 |
| Ethiopian | Zoogeographic realm | endemic | 3570 |
| Géba | River (basin) | misidentification | 43912 |
| Itimbiri | River (basin) | native | 43912 |
| Léfini-Likouala | River (basin) | native | 88782 |
| Lindi-Tshopo | River (basin) | native | 43912 |
| Lomami | River (basin) | native | 106245 |
| Lower Congo | River (basin) | native | 43912 |
| Lualaba | River (basin) | native | 43912 |
| Mai-Ndombe | Lake | native | 43912 |
| Marine Lower Congo | River (basin) | native | 43912 |
| Middle Congo | River (basin) | native | 43912 |
| Niger | River (basin) | misidentification | 43912 |
| Niger Delta | River (basin) | misidentification | 43912 |
| Pool Malebo | Lake | native | 43912 |
| Ruki | River (basin) | native | 43912 |
| Sangha | River (basin) | native | 43912 |
| Sankuru | River (basin) | native | 43912 |
| Ubangui | River (basin) | native | 43912 |
| Upper Lualaba | River (basin) | native | 43912 |
| Wagenia Falls | River (basin) | native | 43912 |