| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Andaman Sea | Sea/Bay/Gulf | native | 3279 |
| Arabian Sea | Sea/Bay/Gulf | native | 2872 |
| Atulayan Bay | Sea/Bay/Gulf | native | 41469 |
| Bay of Bengal | Sea/Bay/Gulf | native | 3279 |
| Chang-hwa | Sea/Bay/Gulf | native | 43515 |
| Chao Phraya River | River (basin) | native | 12693 |
| Chilika Lake/Lagoon | Lagoon | native | 29108 |
| Erhjen River | River (basin) | native | 36073 |
| Ganges | River (basin) | native | 26282 |
| Gulf of Oman | Sea/Bay/Gulf | native | 11441 |
| Gulf of Thailand | Sea/Bay/Gulf | native | 3279 |
| Indian Ocean | Sea/Bay/Gulf | native | 3290 |
| Indonesian Sea | Sea/Bay/Gulf | native | 3279 |
| Kaoping River | River (basin) | native | 36073 |
| Mekong | River (basin) | native | 12693 |
| Oriental | Zoogeographic realm | endemic | 3279 |
| Pacific Ocean | Sea/Bay/Gulf | native | 3279 |
| Panguil Bay | Sea/Bay/Gulf | native | 47626 |
| Shiliao River | River (basin) | native | 36073 |
| Sofronio Española | Sea/Bay/Gulf | native | 114805 |
| South China Sea | Sea/Bay/Gulf | native | 36648 |
| Southern China | Sea/Bay/Gulf | native | 31075 |
| Southern Palawan | Sea/Bay/Gulf | native | 114805 |
| Sulu-Celebes Sea | Sea/Bay/Gulf | native | 393 |
| Tai-chung | Sea/Bay/Gulf | native | 43515 |
| Tanshui River | River (basin) | native | 36073 |
| Tsengwen River | River (basin) | native | 36073 |
| Tung-hsiao | Sea/Bay/Gulf | native | 43515 |
| West Philippine Sea | Sea/Bay/Gulf | native | 130287 |
| Yellow Sea | Sea/Bay/Gulf | native | 4868 |