| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Aruwimi | River (basin) | native | 106290 |
| Congo | River (basin) | native | 41594 |
| Ethiopian | Zoogeographic realm | endemic | 2801 |
| Itimbiri | River (basin) | native | 106290 |
| Kasai | River (basin) | native | 42034 |
| Lindi-Tshopo | River (basin) | endemic | 106290 |
| Lower Congo | River (basin) | native | 42510 |
| Lualaba | River (basin) | native | 83760 |
| Malagarazi | River (basin) | native | 98755 |
| Mweru | Lake | native | 45616 |
| Pool Malebo | Lake | native | 44985 |
| Tanganyika | Lake | native | 4967 |
| Ubangui | River (basin) | native | 45441 |
| Uélé | River (basin) | native | 41594 |
| Upper Lualaba | River (basin) | native | 2970 |
| Wagenia Falls | River (basin) | native | 106245 |