| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Aruwimi River | River (basin) | native | 41594 |
| Congo | River (basin) | native | 2970 |
| Ethiopian | Zoogeographic realm | endemic | 7095 |
| Itimbiri River | River (basin) | native | 106290 |
| Kasai River | River (basin) | native | 46243 |
| Léfini-Likouala Region | River (basin) | native | 44840 |
| Lindi-Tshopo Region | River (basin) | native | 106290 |
| Lower Congo | River (basin) | native | 42510 |
| Lualaba | River (basin) | native | 45616 |
| Mai-Ndombe | Lake | native | 1877 |
| Malagarazi | River (basin) | native | 4967 |
| Malebo Pool | Lake | native | 44985 |
| Marine Lower Congo | River (basin) | native | 1878 |
| Middle Congo | River (basin) | native | 4910 |
| Ruki River Region | River (basin) | native | 93897 |
| Sangha | River (basin) | native | 44840 |
| Sankuru | River (basin) | native | 88943 |
| Tanganyika | Lake | native | 4967 |
| Tumba | Lake | native | 41580 |
| Ubangui | River (basin) | native | 45441 |
| Uélé | River (basin) | native | 41594 |
| Upper Lualaba | River (basin) | native | 2970 |
| Wagenia Falls | River (basin) | native | 106245 |