| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Assal | Lake | native | 47461 |
| Awash | River (basin) | native | 47461 |
| Dhut | River (basin) | native | 47461 |
| Eritrea Coast | River (basin) | native | 47461 |
| Ethiopian | Zoogeographic realm | native | 2064 |
| Gulf of Aden | Sea/Bay/Gulf | native | 117436 |
| Indian Ocean | Sea/Bay/Gulf | native | 27139 |
| Mediterranean Sea | Sea/Bay/Gulf | introduced | 11441 |
| Nile | River (basin) | native | 47461 |
| Northern Red Sea Coast | River (basin) | native | 47461 |
| Obock | River (basin) | native | 47461 |
| Ogaden | River (basin) | native | 47461 |
| Oriental | Zoogeographic realm | native | 51161 |
| Palearctic | Zoogeographic realm | native | 5385 |
| Persian Gulf | Sea/Bay/Gulf | native | 11441 |
| Red Sea | Sea/Bay/Gulf | native | 84159 |
| Siwa Depression | River (basin) | native | 47461 |
| Somali Coast | River (basin) | native | 47461 |
| Somaliland Coast | River (basin) | native | 47461 |
| Tigris | River (basin) | native | 39702 |