| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Andaman Sea | Sea/Bay/Gulf | native | 188 |
| Bay of Bengal | Sea/Bay/Gulf | native | 188 |
| Chilika Lake/Lagoon | Lagoon | native | 95460 |
| Davao Gulf | Sea/Bay/Gulf | native | 43437 |
| Gulf of Thailand | Sea/Bay/Gulf | native | 188 |
| Honda Bay | Sea/Bay/Gulf | native | 71000 |
| Indian Ocean | Sea/Bay/Gulf | native | 188 |
| Lagonoy Gulf | Sea/Bay/Gulf | native | 43283 |
| Leyte Gulf | Sea/Bay/Gulf | native | 31411 |
| Lingayen Gulf | Sea/Bay/Gulf | native | 43020 |
| Pacific Ocean | Sea/Bay/Gulf | native | 188 |
| Pagbilao Bay | Sea/Bay/Gulf | native | 11338 |
| Persian Gulf | Sea/Bay/Gulf | native | 113892 |
| Ragay Gulf | Sea/Bay/Gulf | native | 47919 |
| Ruerhmen River | River (basin) | native | 36073 |
| Samar Sea | Sea/Bay/Gulf | native | 29039 |
| San Miguel Bay | Sea/Bay/Gulf | native | 43275 |
| San Pedro Bay | Sea/Bay/Gulf | native | 46240 |
| Shiliao River | River (basin) | questionable | 36073 |
| Sorsogon Bay | Sea/Bay/Gulf | native | 47531 |
| South China Sea | Sea/Bay/Gulf | native | 36648 |
| Southern Palawan | Sea/Bay/Gulf | native | 114805 |
| Sulu-Celebes Sea | Sea/Bay/Gulf | native | 40726 |
| Tanshui River | River (basin) | native | 36073 |