| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Aruwimi | River (basin) | native | 106290 |
| Bangweulu | River (basin) | native | 248 |
| Congo | River (basin) | native | 248 |
| Edward | Lake | native | 248 |
| Ethiopian | Zoogeographic realm | endemic | 3820 |
| Itimbiri | River (basin) | native | 106290 |
| Kivu | Lake | native | 107916 |
| Kunene | River (basin) | native | 7248 |
| Kwando | River (basin) | native | 33857 |
| Lomami | River (basin) | native | 106245 |
| Lualaba | River (basin) | native | 248 |
| Malagarazi | River (basin) | native | 248 |
| Malawi | Lake | native | 107916 |
| Middle Congo | River (basin) | native | 106245 |
| Mweru | Lake | native | 248 |
| Nile | River (basin) | native | 248 |
| Okavango | River (basin) | native | 7248 |
| Rukwa | Lake | native | 27292 |
| Rusizi | River (basin) | native | 248 |
| Sabaki | River (basin) | introduced | 52331 |
| Shabeelle | River (basin) | questionable | 248 |
| Tana | River (basin) | questionable | 13332 |
| Tanganyika | Lake | native | 248 |
| Ubangui | River (basin) | native | 45441 |
| Uélé | River (basin) | native | 41590 |
| Upper Lualaba | River (basin) | native | 42554 |
| Victoria | Lake | native | 34290 |
| Wagenia Falls | River (basin) | native | 106245 |
| Zambezi | River (basin) | native | 13332 |