| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Bangweulu | River (basin) | native | 42135 |
| Benue | River (basin) | misidentification | 57414 |
| Chad | River (basin) | misidentification | 57414 |
| Chobe | River (basin) | misidentification | 79610 |
| Congo | River (basin) | native | 79609 |
| Edward | Lake | native | 4903 |
| Ethiopian | Zoogeographic realm | endemic | 6803 |
| Linyanti Swamp | Lake | misidentification | 79610 |
| Malagarazi | River (basin) | native | 98755 |
| Niger | River (basin) | misidentification | 57414 |
| Nile | River (basin) | native | 28714 |
| Rusizi | River (basin) | native | 98755 |
| Tanganyika | Lake | native | 7393 |
| Upper Lualaba | River (basin) | native | 79609 |
| Victoria | Lake | native | 34290 |
| Victoria Nile | River (basin) | native | 4903 |
| White Nile | River (basin) | native | 120561 |
| Zambezi | River (basin) | misidentification | 79610 |