| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Congo | River (basin) | native | 93587 |
| Edward | Lake | native | 107916 |
| Ethiopian | Zoogeographic realm | endemic | 2801 |
| Kivu | Lake | native | 107916 |
| Lualaba | River (basin) | native | 93587 |
| Malagarazi | River (basin) | native | 98755 |
| Pangani | River (basin) | native | 27292 |
| Rufiji | River (basin) | native | 4967 |
| Rukwa | Lake | native | 27292 |
| Rusizi | River (basin) | native | 98755 |
| Sabaki | River (basin) | native | 30558 |
| Tanganyika | Lake | native | 107916 |
| Victoria | Lake | native | 27628 |
| Wami | River (basin) | native | 4967 |
| White Nile | River (basin) | native | 4903 |