| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Aruwimi River | River (basin) | native | 106290 |
| Congo | River (basin) | native | 51193 |
| Ethiopian | Zoogeographic realm | endemic | 2829 |
| Itimbiri River | River (basin) | native | 106290 |
| Kasai River | River (basin) | native | 41591 |
| Lindi-Tshopo Region | River (basin) | native | 106290 |
| Lomami River | River (basin) | native | 106245 |
| Lower Congo | River (basin) | native | 42510 |
| Lualaba | River (basin) | native | 106245 |
| Malagarazi | River (basin) | native | 45434 |
| Malebo Pool | Lake | native | 41585 |
| Middle Congo | River (basin) | native | 4910 |
| Sangha | River (basin) | native | 46233 |
| Sankuru | River (basin) | native | 1880 |
| Tanganyika | Lake | native | 2829 |
| Ubangui | River (basin) | native | 45441 |
| Uélé | River (basin) | native | 41594 |
| Upper Lualaba | River (basin) | native | 45434 |
| Wagenia Falls | River (basin) | native | 106245 |