| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Bangweulu | River (basin) | native | 42135 |
| Chobe | River (basin) | native | 37065 |
| Congo | River (basin) | native | 11970 |
| Ethiopian | Zoogeographic realm | endemic | 5682 |
| Etosha | Lake | native | 120641 |
| Kariba | Lake | native | 39194 |
| Kasai | River (basin) | native | 11970 |
| Kunene | River (basin) | native | 11970 |
| Kwando | River (basin) | native | 37065 |
| Kwango | River (basin) | native | 11970 |
| Kwilu | River (basin) | native | 11970 |
| Liambezi | Lake | native | 37065 |
| Limpopo | River (basin) | native | 13337 |
| Linyanti Swamp | Lake | native | 37065 |
| Lower Zambezi | River (basin) | native | 95585 |
| Malawi | Lake | native | 55954 |
| Middle Zambezi | River (basin) | native | 95585 |
| Mweru | Lake | native | 95585 |
| Okavango | River (basin) | native | 11970 |
| Orange | River (basin) | native | 7248 |
| Rukwa | Lake | native | 27292 |
| Upper Lualaba | River (basin) | native | 2970 |
| Upper Zambezi | River (basin) | native | 11970 |
| Wagenia Falls | River (basin) | native | 106245 |
| Zambezi | River (basin) | native | 5682 |