| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Aruwimi | River (basin) | native | 106290 |
| Chiloango | River (basin) | questionable | 41591 |
| Congo | River (basin) | endemic | 42019 |
| Ethiopian | Zoogeographic realm | endemic | 5331 |
| Itimbiri | River (basin) | native | 106290 |
| Léfini-Likouala | River (basin) | native | 88782 |
| Lualaba | River (basin) | native | 42019 |
| Mai-Ndombe | Lake | native | 42019 |
| Middle Congo | River (basin) | native | 41590 |
| Ruki | River (basin) | native | 93897 |
| Sangha | River (basin) | native | 42019 |
| Tumba | Lake | native | 44984 |
| Uélé | River (basin) | native | 42019 |
| Upper Lualaba | River (basin) | native | 45616 |