| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Agulhas Current | Sea/Bay/Gulf | native | 55 |
| Andaman Sea | Sea/Bay/Gulf | native | 55 |
| Arabian Sea | Sea/Bay/Gulf | native | 55 |
| Atlantic Ocean | Sea/Bay/Gulf | native | 55 |
| Australian | Zoogeographic realm | native | 2847 |
| Bay of Bengal | Sea/Bay/Gulf | native | 55 |
| Carigara Bay | Sea/Bay/Gulf | native | 46323 |
| Chiku River | River (basin) | native | 36073 |
| Chilika Lake/Lagoon | Lagoon | native | 29108 |
| Coral Sea and GBR | Sea/Bay/Gulf | native | 55 |
| East Central Australian Shelf | Sea/Bay/Gulf | native | 55 |
| East China Sea | Sea/Bay/Gulf | native | 47843 |
| Erhjen River | River (basin) | native | 36073 |
| Great Barrier Reef | Sea/Bay/Gulf | native | 55 |
| Gulf of Aden | Sea/Bay/Gulf | native | 55 |
| Gulf of Oman | Sea/Bay/Gulf | native | 55 |
| Gulf of Thailand | Sea/Bay/Gulf | native | 55 |
| Indian Ocean | Sea/Bay/Gulf | native | 55 |
| Indonesian Sea | Sea/Bay/Gulf | native | 7050 |
| Kaoping River | River (basin) | native | 36073 |
| Kimbe Bay | Sea/Bay/Gulf | native | 28888 |
| Kuroshio Current | Sea/Bay/Gulf | native | 559 |
| Lagonoy Gulf | Sea/Bay/Gulf | native | 43283 |
| Lake Mainit | Lake | native | 4867 |
| Lanuza Bay | Sea/Bay/Gulf | native | 104756 |
| Lingayen Gulf | Sea/Bay/Gulf | native | 5399 |
| Mediterranean Sea | Sea/Bay/Gulf | introduced | 55 |
| Milne Bay | Sea/Bay/Gulf | native | 41464 |
| Naujan Lake | Lake | native | 13446 |
| North Australian Shelf | Sea/Bay/Gulf | native | 55 |
| Northwest Australian Shelf | Sea/Bay/Gulf | native | 38544 |
| Oriental | Zoogeographic realm | native | 5399 |
| Pacific Ocean | Sea/Bay/Gulf | native | 55 |
| Pagbilao Bay | Sea/Bay/Gulf | native | 11338 |
| Panay Gulf | Sea/Bay/Gulf | native | 42831 |
| Panguil Bay | Sea/Bay/Gulf | native | 47626 |
| Peng-hu Island | Sea/Bay/Gulf | native | 55073 |
| Persian Gulf | Sea/Bay/Gulf | native | 55 |
| Polynesian Waters | Sea/Bay/Gulf | native | 55 |
| Ragay Gulf | Sea/Bay/Gulf | native | 47919 |
| Red Sea | Sea/Bay/Gulf | native | 84159 |
| Ruerhmen River | River (basin) | native | 36073 |
| San Miguel Bay | Sea/Bay/Gulf | native | 43275 |
| Shihtsao River | River (basin) | native | 36073 |
| Shiliao River | River (basin) | native | 36073 |
| Sikao Creek | River (basin) | native | 52823 |
| Somali Coastal Current | Sea/Bay/Gulf | native | 55 |
| South China Sea | Sea/Bay/Gulf | native | 36648 |
| South West Australian Shelf | Sea/Bay/Gulf | native | 55 |
| Southern China | Sea/Bay/Gulf | native | 119494 |
| Southern Palawan | Sea/Bay/Gulf | native | 114805 |
| Taal Lake | Lake | native | 12165 |
| Tanshui River | River (basin) | native | 36073 |
| Tsengwen River | River (basin) | native | 36073 |
| Tubbataha Reefs | Sea/Bay/Gulf | native | 53416 |
| Tung-hsiao | Sea/Bay/Gulf | native | 43510 |
| West Central Australian Shelf | Sea/Bay/Gulf | native | 55 |
| Yellow Sea | Sea/Bay/Gulf | native | 55 |