| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Aruwimi River | River (basin) | introduced | 106290 |
| Australian | Zoogeographic realm | introduced | 12108 |
| Chobe | River (basin) | native | 37065 |
| Congo | River (basin) | native | 2 |
| Ethiopian | Zoogeographic realm | endemic | 58 |
| Kariba | Lake | introduced | 27602 |
| Kasai River | River (basin) | native | 2 |
| Kivu | Lake | introduced | 27629 |
| Kunene | River (basin) | native | 33857 |
| Kwando River | River (basin) | native | 37065 |
| Liambezi | Lake | native | 37065 |
| Limpopo | River (basin) | introduced | 54042 |
| Linyanti Swamp | Lake | native | 37065 |
| Luapula | River (basin) | native | 95585 |
| Middle Zambezi | River (basin) | native | 95585 |
| Mweru | Lake | native | 2989 |
| Okavango | River (basin) | native | 54974 |
| Palearctic | Zoogeographic realm | introduced | 56698 |
| Upper Lualaba | River (basin) | native | 2970 |
| Upper Zambezi | River (basin) | native | 11970 |
| Zambezi | River (basin) | native | 13332 |