| Ecosysteem | Type | Status | Ref. |
|---|---|---|---|
| Aruwimi River | River (basin) | native | 44050 |
| Bomu | River (basin) | native | 44050 |
| Congo | River (basin) | endemic | 78218 |
| Ethiopian | Zoogeographic realm | endemic | 34006 |
| Itimbiri River | River (basin) | native | 44050 |
| Kasai River | River (basin) | native | 44050 |
| Kotto River | River (basin) | native | 44050 |
| Kwilu River | River (basin) | native | 44050 |
| Lindi-Tshopo Region | River (basin) | native | 44050 |
| Lower Congo | River (basin) | native | 44050 |
| Lualaba | River (basin) | native | 44050 |
| Lukenie | River (basin) | native | 44050 |
| Malebo Pool | Lake | native | 44050 |
| Middle Congo | River (basin) | native | 44050 |
| Mongala | River (basin) | native | 44050 |
| Ruki River Region | River (basin) | native | 44050 |
| Ubangui | River (basin) | native | 44050 |
| Uélé | River (basin) | native | 44050 |
| Upper Lualaba | River (basin) | native | 44050 |
| Wagenia Falls | River (basin) | native | 106245 |