| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Aruwimi River | River (basin) | native | 82238 |
| Congo | River (basin) | endemic | 82238 |
| Ethiopian | Zoogeographic realm | endemic | 3202 |
| Itimbiri River | River (basin) | native | 82238 |
| Kasai River | River (basin) | native | 82238 |
| Kwango River | River (basin) | native | 82238 |
| Lomami River | River (basin) | native | 82238 |
| Lualaba | River (basin) | native | 82238 |
| Lukenie | River (basin) | native | 82238 |
| Mai-Ndombe | Lake | native | 2988 |
| Malebo Pool | Lake | native | 82238 |
| Marine Lower Congo | River (basin) | native | 82238 |
| Middle Congo | River (basin) | native | 82238 |
| Mongala | River (basin) | native | 82238 |
| Ogowe | River (basin) | questionable | 82238 |
| Ruki River Region | River (basin) | native | 82238 |
| Sangha | River (basin) | native | 51193 |
| Sankuru | River (basin) | native | 82238 |
| Ubangui | River (basin) | native | 82238 |
| Uélé | River (basin) | native | 82238 |
| Upper Lualaba | River (basin) | native | 82238 |
| Wagenia Falls | River (basin) | native | 106245 |