| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Agulhas Current | Sea/Bay/Gulf | native | 5213 |
| Andaman Sea | Sea/Bay/Gulf | native | 5736 |
| Arabian Sea | Sea/Bay/Gulf | native | 2872 |
| Atlantic Ocean | Sea/Bay/Gulf | native | 1602 |
| Australian | Zoogeographic realm | native | 7300 |
| Bay of Bengal | Sea/Bay/Gulf | native | 1479 |
| Bensbach River | River (basin) | native | 50786 |
| Cauvery | River (basin) | native | 43636 |
| Chiku River | River (basin) | native | 36073 |
| Chilika Lake/Lagoon | Lagoon | native | 29108 |
| Coral Sea and GBR | Sea/Bay/Gulf | native | 1602 |
| Davao Gulf | Sea/Bay/Gulf | native | 43437 |
| East China Sea | Sea/Bay/Gulf | native | 1602 |
| Ethiopian | Zoogeographic realm | native | 3501 |
| Fitzroy | River (basin) | native | 84364 |
| Gulf of Aden | Sea/Bay/Gulf | native | 1602 |
| Gulf of Thailand | Sea/Bay/Gulf | native | 4537 |
| Indian Ocean | Sea/Bay/Gulf | native | 1602 |
| Indonesian Sea | Sea/Bay/Gulf | native | 5978 |
| Kaoping River | River (basin) | native | 36073 |
| Kuroshio Current | Sea/Bay/Gulf | native | 559 |
| Lagonoy Gulf | Sea/Bay/Gulf | native | 43283 |
| Laguna de Bay | Lake | native | 13460 |
| Lake Mainit | Lake | native | 4867 |
| Mekong | River (basin) | native | 12693 |
| Naujan Lake | Lake | native | 13446 |
| North Australian Shelf | Sea/Bay/Gulf | native | 7300 |
| Northeast Australian Shelf | Sea/Bay/Gulf | native | 7300 |
| Northwest Australian Shelf | Sea/Bay/Gulf | native | 7300 |
| Oriental | Zoogeographic realm | native | 45255 |
| Ormoc Bay | Sea/Bay/Gulf | native | 45205 |
| Pacific Ocean | Sea/Bay/Gulf | native | 592 |
| Pagbilao Bay | Sea/Bay/Gulf | native | 11338 |
| 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 | 1602 |
| Red Sea | Sea/Bay/Gulf | native | 84159 |
| Ruerhmen River | River (basin) | native | 36073 |
| Sabaki | River (basin) | native | 30558 |
| Samar Sea | Sea/Bay/Gulf | native | 29039 |
| San Miguel Bay | Sea/Bay/Gulf | native | 43275 |
| Sea of Japan/East Sea | Sea/Bay/Gulf | native | 559 |
| Shihtsao River | River (basin) | native | 36073 |
| Shiliao River | River (basin) | native | 36073 |
| Somali Coastal Current | Sea/Bay/Gulf | native | 12484 |
| 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 | 4867 |
| Taal Lake | Lake | native | 12165 |
| Tana | River (basin) | native | 52331 |
| Tañon Strait | Sea/Bay/Gulf | native | 280 |
| Tanshui River | River (basin) | native | 36073 |
| Tung-hsiao | Sea/Bay/Gulf | native | 43510 |
| Yellow Sea | Sea/Bay/Gulf | native | 4868 |
| Zambezi | River (basin) | native | 39194 |