| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Bangweulu | River (basin) | native | 45616 |
| Chobe | River (basin) | native | 37065 |
| Congo | River (basin) | native | 2970 |
| Ethiopian | Zoogeographic realm | endemic | 6060 |
| Kwando | River (basin) | native | 37065 |
| Lualaba | River (basin) | native | 80296 |
| Malagarazi | River (basin) | native | 54847 |
| Mweru | Lake | native | 45616 |
| Okavango | River (basin) | native | 7248 |
| Rufiji | River (basin) | native | 89002 |
| Rukwa | Lake | native | 27292 |
| Rusizi | River (basin) | native | 87863 |
| Sabaki | River (basin) | native | 52331 |
| Tana | Lake | questionable | 52331 |
| Tanganyika | Lake | native | 56055 |
| Upper Lualaba | River (basin) | native | 2970 |
| Upper Zambezi | River (basin) | native | 7248 |
| Victoria | Lake | native | 34290 |
| Victoria Nile | River (basin) | native | 4903 |
| Zambezi | River (basin) | native | 7248 |