| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Atulayan Bay | Sea/Bay/Gulf | native | 41469 |
| Australian | Zoogeographic realm | native | 2847 |
| Bensbach River | River (basin) | native | 50786 |
| Chilika Lake/Lagoon | Lagoon | native | 95460 |
| Lagonoy Gulf | Sea/Bay/Gulf | native | 43283 |
| Laguna de Bay | Lake | native | 13460 |
| Lake Lanao | Lake | questionable | 13446 |
| Mekong | River (basin) | native | 12693 |
| Oriental | Zoogeographic realm | native | 4833 |
| Sorsogon Bay | Sea/Bay/Gulf | native | 47531 |
| South China Sea | Sea/Bay/Gulf | native | 36648 |