| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Bangweulu | River (basin) | native | 78218 |
| Buzi | River (basin) | native | 13332 |
| Congo | River (basin) | native | 87869 |
| Ethiopian | Zoogeographic realm | endemic | 3818 |
| Incomati | River (basin) | native | 13332 |
| Kivu | Lake | native | 46152 |
| Limpopo | River (basin) | native | 13332 |
| Lower Zambezi | River (basin) | native | 95585 |
| Lualaba | River (basin) | native | 80298 |
| Maputo | River (basin) | native | 78218 |
| Mweru | Lake | native | 78218 |
| Okavango | River (basin) | native | 13332 |
| Pangani | River (basin) | misidentification | 78218 |
| Pungwe | River (basin) | native | 13332 |
| Rufiji | River (basin) | native | 78218 |
| Rukwa | Lake | native | 27292 |
| Rusizi | River (basin) | native | 87863 |
| Sabaki | River (basin) | misidentification | 85045 |
| Sabi | River (basin) | native | 13332 |
| Shabeelle | River (basin) | misidentification | 85045 |
| Tana | River (basin) | misidentification | 85045 |
| Tanganyika | Lake | native | 87863 |
| Upper Lualaba | River (basin) | native | 78218 |
| Upper Zambezi | River (basin) | native | 95585 |
| Victoria | Lake | native | 52331 |
| Wami | River (basin) | native | 27292 |
| Zambezi | River (basin) | native | 13337 |