| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Chiku River | River (basin) | native | 36073 |
| East China Sea | Sea/Bay/Gulf | native | 47843 |
| Indian Ocean | Sea/Bay/Gulf | native | 2798 |
| Indonesian Sea | Sea/Bay/Gulf | native | 5978 |
| Kaoping River | River (basin) | native | 36073 |
| Ormoc Bay | Sea/Bay/Gulf | native | 45205 |
| Pacific Ocean | Sea/Bay/Gulf | native | 28614 |
| Panguil Bay | Sea/Bay/Gulf | native | 47626 |
| Ruerhmen River | River (basin) | native | 36073 |
| San Miguel Bay | Sea/Bay/Gulf | native | 45674 |
| Shihtsao River | River (basin) | native | 36073 |
| Shiliao River | River (basin) | native | 36073 |
| South China Sea | Sea/Bay/Gulf | native | 36648 |
| Taal Lake | Lake | native | 13446 |
| Tanshui River | River (basin) | native | 36073 |
| Tsengwen River | River (basin) | native | 36073 |