| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Bangweulu | River (basin) | native | 95585 |
| Baringo | Lake | questionable | 49139 |
| Buzi | River (basin) | native | 94654 |
| Chobe | River (basin) | native | 33857 |
| Congo | River (basin) | native | 27609 |
| Edward | Lake | native | 4903 |
| Ethiopian | Zoogeographic realm | endemic | 2801 |
| Kivu | Lake | native | 107916 |
| Kunene | River (basin) | native | 7248 |
| Lower Zambezi | River (basin) | native | 95585 |
| Middle Zambezi | River (basin) | native | 95585 |
| Mweru | Lake | native | 27609 |
| Okavango | River (basin) | native | 7248 |
| Pangani | River (basin) | native | 52331 |
| Pungwe | River (basin) | native | 94654 |
| Rufiji | River (basin) | native | 41366 |
| Sabaki | River (basin) | native | 52331 |
| Sabi | River (basin) | native | 7248 |
| Shire | River (basin) | native | 37112 |
| Tana | River (basin) | native | 52331 |
| Tanganyika | Lake | native | 4967 |
| Upper Lualaba | River (basin) | native | 2970 |
| Upper Zambezi | River (basin) | native | 95585 |
| Victoria | Lake | native | 52331 |
| Victoria Nile | River (basin) | native | 4903 |
| Wami | River (basin) | native | 41366 |
| Zambezi | River (basin) | native | 13332 |