| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Aruwimi | River (basin) | native | 74421 |
| Congo | River (basin) | native | 74421 |
| Ethiopian | Zoogeographic realm | endemic | 5331 |
| Itimbiri | River (basin) | native | 106290 |
| Kasai | River (basin) | native | 11970 |
| Kivu | Lake | error | 107916 |
| Kouilou-Niari | River (basin) | native | 80290 |
| Lindi-Tshopo | River (basin) | native | 1878 |
| Lobé | River (basin) | native | 80290 |
| Lualaba | River (basin) | native | 45434 |
| Lulonga | River (basin) | native | 41591 |
| Mai-Ndombe | Lake | native | 1879 |
| Malagarazi | River (basin) | native | 54847 |
| Marine Lower Congo | River (basin) | native | 74421 |
| Middle Congo | River (basin) | native | 4910 |
| Nkomi | River (basin) | native | 80290 |
| Ntem | River (basin) | native | 80290 |
| Nyong | River (basin) | native | 80290 |
| Ogowe | River (basin) | native | 80290 |
| Pool Malebo | Lake | native | 74421 |
| Ruki | River (basin) | native | 93897 |
| Sangha | River (basin) | native | 74421 |
| Sankuru | River (basin) | native | 11970 |
| Ubangui | River (basin) | native | 45441 |
| Uélé | River (basin) | native | 41594 |
| Wagenia Falls | River (basin) | native | 106245 |