| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Australian | Zoogeographic realm | native | 5259 |
| Lake Lanao | Lake | native | 95183 |
| Naujan Lake | Lake | native | 13446 |
| Oriental | Zoogeographic realm | native | 2847 |
| Pagbilao Bay | Sea/Bay/Gulf | native | 11338 |
| Panguil Bay | Sea/Bay/Gulf | native | 47626 |
| Ragay Gulf | Sea/Bay/Gulf | native | 47919 |
| Ruerhmen River | River (basin) | native | 36073 |
| South China Sea | Sea/Bay/Gulf | native | 36648 |
| Taal Lake | Lake | native | 12165 |
| Tsengwen River | River (basin) | native | 36073 |