| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Bangweulu | River (basin) | native | 248 |
| Chad | River (basin) | native | 367 |
| Chobe | River (basin) | native | 37065 |
| Congo | River (basin) | native | 248 |
| Cuanza | River (basin) | native | 120641 |
| Ethiopian | Zoogeographic realm | endemic | 248 |
| Incomati | River (basin) | native | 3820 |
| Kasai | River (basin) | native | 248 |
| Kunene | River (basin) | native | 52863 |
| Kwando | River (basin) | native | 37065 |
| Kwango | River (basin) | native | 248 |
| Liambezi | Lake | native | 37065 |
| Limpopo | River (basin) | native | 13332 |
| Linyanti Swamp | Lake | native | 37065 |
| Lower Zambezi | River (basin) | native | 95585 |
| Malawi | Lake | native | 55909 |
| Maputo | River (basin) | native | 7248 |
| Middle Congo | River (basin) | native | 248 |
| Middle Zambezi | River (basin) | native | 95585 |
| Mweru | Lake | native | 248 |
| Okavango | River (basin) | native | 248 |
| Pungwe | River (basin) | native | 248 |
| Ruki | River (basin) | native | 93897 |
| Sabi | River (basin) | native | 248 |
| Sankuru | River (basin) | native | 248 |
| Shire | River (basin) | native | 37112 |
| Sibaya | Lake | native | 3820 |
| Tanganyika | Lake | native | 248 |
| Ubangui | River (basin) | native | 248 |
| Umgeni | River (basin) | native | 3820 |
| Upper Lualaba | River (basin) | native | 248 |
| Upper Zambezi | River (basin) | native | 95585 |
| Zambezi | River (basin) | native | 248 |