| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Aruwimi | River (basin) | native | 80450 |
| Bangweulu | River (basin) | native | 95585 |
| Congo | River (basin) | native | 80290 |
| Cross | River (basin) | native | 80290 |
| Dibamba | River (basin) | native | 80290 |
| Ethiopian | Zoogeographic realm | endemic | 2880 |
| Itimbiri | River (basin) | native | 106290 |
| Kasai | River (basin) | native | 11970 |
| Kouilou-Niari | River (basin) | native | 80290 |
| Lindi-Tshopo | River (basin) | native | 106290 |
| Lokoundje | River (basin) | native | 80290 |
| Lualaba | River (basin) | native | 80290 |
| Malagarazi | River (basin) | native | 36901 |
| Middle Congo | River (basin) | native | 80450 |
| Mweru | Lake | native | 80290 |
| Ntem | River (basin) | native | 80290 |
| Nyanga | River (basin) | native | 80290 |
| Ogowe | River (basin) | native | 80290 |
| Pool Malebo | Lake | native | 42019 |
| Rusizi | River (basin) | native | 98755 |
| Sanaga | River (basin) | native | 80290 |
| Sangha | River (basin) | native | 80450 |
| Sankuru | River (basin) | native | 13455 |
| Tanganyika | Lake | native | 36901 |
| Ubangui | River (basin) | native | 45441 |
| Uélé | River (basin) | native | 41594 |
| Upper Lualaba | River (basin) | native | 80290 |
| Wagenia Falls | River (basin) | native | 106245 |
| Wouri | River (basin) | native | 80290 |