| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Abaya | Lake | native | 58532 |
| Aruwimi | River (basin) | questionable | 58532 |
| Awash | River (basin) | native | 58460 |
| Benue | River (basin) | native | 58532 |
| Blue Nile | River (basin) | native | 28714 |
| Chad | River (basin) | native | 81282 |
| Congo | River (basin) | questionable | 58532 |
| Ethiopian | Zoogeographic realm | endemic | 2801 |
| Kwango | River (basin) | questionable | 58532 |
| Lindi-Tshopo | River (basin) | questionable | 58532 |
| Lower Congo | River (basin) | questionable | 58532 |
| Niger | River (basin) | native | 58532 |
| Nile | River (basin) | native | 58532 |
| Northern Ethiopian Rift | Lake | native | 58532 |
| Pangani | River (basin) | native | 58532 |
| Sabaki | River (basin) | native | 30558 |
| Sanaga | River (basin) | native | 81639 |
| Shabeelle | River (basin) | native | 58532 |
| Tana | River (basin) | native | 52331 |
| Tana | Lake | native | 58532 |
| Turkana | Lake | native | 58460 |
| Uélé | River (basin) | questionable | 58532 |
| Victoria | Lake | native | 34290 |
| Victoria Nile | River (basin) | native | 4903 |
| White Nile | River (basin) | native | 28714 |