| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Bangweulu | River (basin) | native | 55074 |
| Chobe | River (basin) | native | 37065 |
| Congo | River (basin) | native | 55074 |
| Cuanza | River (basin) | questionable | 120641 |
| Ethiopian | Zoogeographic realm | endemic | 5163 |
| Etosha | Lake | native | 120641 |
| Great Fish | River (basin) | introduced | 94788 |
| Kasai | River (basin) | native | 55074 |
| Kunene | River (basin) | native | 11970 |
| Kwando | River (basin) | native | 37065 |
| Kwango | River (basin) | native | 55074 |
| Kwilu | River (basin) | native | 11970 |
| Liambezi | Lake | native | 37065 |
| Limpopo | River (basin) | native | 55074 |
| Linyanti Swamp | Lake | native | 37065 |
| Lomami | River (basin) | native | 106245 |
| Lower Zambezi | River (basin) | native | 95585 |
| Lualaba | River (basin) | native | 55074 |
| Malawi | Lake | native | 118638 |
| Middle Zambezi | River (basin) | native | 95585 |
| Mweru | Lake | native | 55074 |
| Okavango | River (basin) | native | 55074 |
| Orange | River (basin) | native | 33857 |
| Palearctic | Zoogeographic realm | introduced | 6094 |
| Rufiji | River (basin) | native | 118638 |
| Rukwa | Lake | native | 118638 |
| Upper Lualaba | River (basin) | native | 55074 |
| Upper Zambezi | River (basin) | native | 95585 |
| Zambezi | River (basin) | native | 55074 |