| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Bangweulu | River (basin) | introduced | 95585 |
| Chobe | River (basin) | native | 37065 |
| Congo | River (basin) | introduced | 41594 |
| Cuanza | River (basin) | native | 42034 |
| Ethiopian | Zoogeographic realm | endemic | 21 |
| Etosha | Lake | native | 120641 |
| Kariba | Lake | native | 54048 |
| Kasai | River (basin) | native | 120641 |
| Kunene | River (basin) | native | 52863 |
| Kwando | River (basin) | native | 37065 |
| Liambezi | Lake | native | 37065 |
| Limpopo | River (basin) | introduced | 54042 |
| Linyanti Swamp | Lake | native | 37065 |
| Middle Zambezi | River (basin) | native | 95585 |
| Mweru | Lake | introduced | 1978 |
| Okavango | River (basin) | native | 52307 |
| Ubangui | River (basin) | introduced | 55074 |
| Upper Zambezi | River (basin) | native | 95585 |
| Zambezi | River (basin) | native | 52307 |