| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Andaman Sea | Sea/Bay/Gulf | native | 5736 |
| Arabian Sea | Sea/Bay/Gulf | native | 2872 |
| Australian | Zoogeographic realm | native | 6390 |
| Bay of Bengal | Sea/Bay/Gulf | native | 1479 |
| Bensbach River | River (basin) | native | 50786 |
| Carigara Bay | Sea/Bay/Gulf | native | 46323 |
| Chilika Lake/Lagoon | Lagoon | native | 29108 |
| Coral Sea and GBR | Sea/Bay/Gulf | native | 5259 |
| Davao Gulf | Sea/Bay/Gulf | native | 45419 |
| Fitzroy | River (basin) | native | 84364 |
| Great Barrier Reef | Sea/Bay/Gulf | native | 9799 |
| Gulf of Thailand | Sea/Bay/Gulf | native | 3281 |
| Indian Ocean | Sea/Bay/Gulf | native | 9799 |
| Indonesian Sea | Sea/Bay/Gulf | native | 2847 |
| Lagonoy Gulf | Sea/Bay/Gulf | native | 43283 |
| Lake Mainit | Lake | native | 81829 |
| Lingayen Gulf | Sea/Bay/Gulf | native | 45866 |
| Mekong | River (basin) | native | 12693 |
| Naujan Lake | Lake | native | 13446 |
| North Australian Shelf | Sea/Bay/Gulf | native | 6390 |
| Northeast Australian Shelf | Sea/Bay/Gulf | native | 6390 |
| Northwest Australian Shelf | Sea/Bay/Gulf | native | 6390 |
| Oriental | Zoogeographic realm | native | 1479 |
| Pacific Ocean | Sea/Bay/Gulf | native | 6390 |
| Palearctic | Zoogeographic realm | native | 3281 |
| Panguil Bay | Sea/Bay/Gulf | native | 47626 |
| Ragay Gulf | Sea/Bay/Gulf | native | 47919 |
| Ruerhmen River | River (basin) | native | 36073 |
| San Miguel Bay | Sea/Bay/Gulf | native | 43275 |
| Shihtsao River | River (basin) | native | 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 | 12547 |
| Tahiti Basins | River (basin) | introduced | 9420 |
| Tonle Sap | Lake | native | 36654 |
| Yellow Sea | Sea/Bay/Gulf | native | 3281 |