| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Buzi | River (basin) | native | 94473 |
| Chobe | River (basin) | native | 37065 |
| Congo | River (basin) | native | 2970 |
| Ethiopian | Zoogeographic realm | endemic | 3203 |
| Incomati | River (basin) | native | 13332 |
| Kariba | Lake | native | 39194 |
| Kasai River | River (basin) | misidentification | 42554 |
| Kunene | River (basin) | native | 52965 |
| Kwando River | River (basin) | native | 37065 |
| Lake Malawi | Lake | native | 55909 |
| Lake Rukwa | Lake | native | 95585 |
| Liambezi | Lake | native | 37065 |
| Limpopo | River (basin) | native | 13332 |
| Linyanti Swamp | Lake | native | 37065 |
| Lower Zambezi | River (basin) | native | 95585 |
| Lualaba | River (basin) | native | 45434 |
| Luapula | River (basin) | native | 95585 |
| Malebo Pool | Lake | misidentification | 41585 |
| Melela | River (basin) | native | 75962 |
| Middle Congo | River (basin) | questionable | 4910 |
| Middle Zambezi | River (basin) | native | 95585 |
| Mweru | Lake | native | 46251 |
| Nile | River (basin) | native | 4906 |
| Okavango | River (basin) | native | 3203 |
| Pungwe | River (basin) | native | 75962 |
| Ruvuma River | River (basin) | misidentification | 95448 |
| Sabaki | River (basin) | native | 13332 |
| Shire | River (basin) | native | 75962 |
| Tana River | River (basin) | questionable | 52331 |
| Upper Lualaba | River (basin) | native | 2970 |
| Upper Zambezi | River (basin) | native | 95585 |
| Victoria | Lake | questionable | 31740 |
| Wagenia Falls | River (basin) | native | 106245 |
| Zambezi | River (basin) | native | 94473 |