| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Buzi | River (basin) | native | 105015 |
| Chobe | River (basin) | native | 37065 |
| Congo | River (basin) | native | 27292 |
| Cuanza | River (basin) | native | 27292 |
| Ethiopian | Zoogeographic realm | endemic | 2801 |
| Incomati | River (basin) | native | 27292 |
| Kasai River | River (basin) | native | 11970 |
| Kunene | River (basin) | native | 52965 |
| Kwando River | River (basin) | native | 37065 |
| Lake Malawi | Lake | native | 55909 |
| Lake Rukwa | Lake | native | 27292 |
| Liambezi | Lake | native | 37065 |
| Limpopo | River (basin) | native | 27292 |
| Lower Zambezi | River (basin) | native | 95585 |
| Luapula | River (basin) | native | 42135 |
| Malagarazi | River (basin) | native | 54847 |
| Mekong | River (basin) | questionable | 33782 |
| Middle Zambezi | River (basin) | native | 95585 |
| Mweru | Lake | native | 41590 |
| Okavango | River (basin) | native | 27501 |
| Pangani | River (basin) | native | 41366 |
| Pongolo | River (basin) | native | 7248 |
| Pungwe | River (basin) | native | 105015 |
| Rufiji | River (basin) | native | 4967 |
| Ruvuma River | River (basin) | native | 4967 |
| Sabi | River (basin) | native | 94654 |
| Shire | River (basin) | native | 37112 |
| Tana River | River (basin) | native | 52331 |
| Upper Lualaba | River (basin) | native | 12818 |
| Upper Zambezi | River (basin) | native | 95585 |
| Victoria | Lake | native | 38676 |
| Wami | River (basin) | native | 4967 |
| White Nile | River (basin) | native | 4903 |
| Zambezi | River (basin) | native | 7248 |