| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Arabian Sea | Sea/Bay/Gulf | native | 2872 |
| Bay of Bengal | Sea/Bay/Gulf | native | 1479 |
| 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 | 4537 |
| Davao Gulf | Sea/Bay/Gulf | native | 43437 |
| East China Sea | Sea/Bay/Gulf | native | 47843 |
| Erhjen River | River (basin) | native | 36073 |
| Euphrates and Tigris Delta | River (basin) | native | 115344 |
| Godavari | River (basin) | native | 51036 |
| Gulf of Oman | Sea/Bay/Gulf | native | 47613 |
| Indian Ocean | Sea/Bay/Gulf | native | 1602 |
| Indonesian Sea | Sea/Bay/Gulf | native | 1602 |
| Kimbe Bay | Sea/Bay/Gulf | native | 28888 |
| Kuroshio Current | Sea/Bay/Gulf | native | 559 |
| Laguna de Bay | Lake | native | 80824 |
| Lake Mainit | Lake | native | 81829 |
| Malacca Strait | Sea/Bay/Gulf | native | 121464 |
| Manila Bay | Sea/Bay/Gulf | native | 35686 |
| Mediterranean Sea | Sea/Bay/Gulf | introduced | 95718 |
| Mekong | River (basin) | native | 12693 |
| Milne Bay | Sea/Bay/Gulf | native | 41464 |
| Naujan Lake | Lake | native | 13446 |
| North Australian Shelf | Sea/Bay/Gulf | native | 4537 |
| Northeast Australian Shelf | Sea/Bay/Gulf | native | 4537 |
| Oriental | Zoogeographic realm | native | 4833 |
| Ormoc Bay | Sea/Bay/Gulf | native | 45140 |
| Pacific Ocean | Sea/Bay/Gulf | native | 4537 |
| Pagbilao Bay | Sea/Bay/Gulf | native | 11338 |
| Palearctic | Zoogeographic realm | native | 4833 |
| Panguil Bay | Sea/Bay/Gulf | native | 47626 |
| Peng-hu Island | Sea/Bay/Gulf | native | 55073 |
| Persian Gulf | Sea/Bay/Gulf | native | 1602 |
| Polynesian Waters | Sea/Bay/Gulf | native | 2847 |
| 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 |
| Shiliao River | River (basin) | native | 36073 |
| Sikao Creek | River (basin) | native | 52823 |
| Sogod Bay | Sea/Bay/Gulf | native | 46392 |
| Sorsogon Bay | Sea/Bay/Gulf | native | 47531 |
| South China Sea | Sea/Bay/Gulf | native | 36648 |
| Southern China | Sea/Bay/Gulf | native | 119494 |
| Southern Palawan | Sea/Bay/Gulf | native | 114805 |
| Sulu-Celebes Sea | Sea/Bay/Gulf | native | 130287 |
| Taal Lake | Lake | native | 12165 |
| Tahiti I. | Sea/Bay/Gulf | native | 4537 |
| Tanshui River | River (basin) | native | 36073 |
| Tayabas Bay | Sea/Bay/Gulf | native | 47573 |
| Tsengwen River | River (basin) | native | 36073 |
| Verde Island Passage | Sea/Bay/Gulf | native | 6956 |
| West Philippine Sea | Sea/Bay/Gulf | native | 130287 |
| Yellow Sea | Sea/Bay/Gulf | native | 4868 |