| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Bangweulu | River (basin) | questionable | 58032 |
| Buzi | River (basin) | misidentification | 86935 |
| Congo | River (basin) | questionable | 58032 |
| Edward | Lake | native | 51287 |
| Ethiopian | Zoogeographic realm | endemic | 3236 |
| Kunene | River (basin) | misidentification | 86935 |
| Limpopo | River (basin) | misidentification | 86935 |
| Lower Zambezi | River (basin) | misidentification | 86935 |
| Lualaba | River (basin) | questionable | 58032 |
| Malagarazi | River (basin) | questionable | 86935 |
| Malawi | Lake | misidentification | 86935 |
| Middle Zambezi | River (basin) | misidentification | 86935 |
| Mweru | Lake | questionable | 58032 |
| Okavango | River (basin) | misidentification | 86935 |
| Pungwe | River (basin) | misidentification | 86935 |
| Rufiji | River (basin) | native | 86935 |
| Rukwa | Lake | native | 27292 |
| Ruvuma | River (basin) | questionable | 86935 |
| Sabi | River (basin) | misidentification | 86935 |
| Southern East Rift Valley | Lake | native | 86935 |
| Tana | River (basin) | questionable | 52331 |
| Upper Lualaba | River (basin) | questionable | 58032 |
| Upper Zambezi | River (basin) | questionable | 86935 |
| Victoria | Lake | questionable | 52331 |
| Zambezi | River (basin) | questionable | 86935 |