| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Agulhas Current | Sea/Bay/Gulf | native | 5213 |
| Atulayan Bay | Sea/Bay/Gulf | native | 41469 |
| Australian | Zoogeographic realm | native | 6192 |
| Bay of Bengal | Sea/Bay/Gulf | native | 1479 |
| Chiku River | River (basin) | native | 36073 |
| Chilika Lake/Lagoon | Lagoon | native | 29108 |
| Coral Sea and GBR | Sea/Bay/Gulf | native | 4959 |
| Erhjen River | River (basin) | native | 36073 |
| Ethiopian | Zoogeographic realm | native | 5213 |
| Gulf of Aden | Sea/Bay/Gulf | native | 5450 |
| Gulf of Oman | Sea/Bay/Gulf | native | 47613 |
| Honda Bay | Sea/Bay/Gulf | native | 71000 |
| Indian Ocean | Sea/Bay/Gulf | native | 3424 |
| Indonesian Sea | Sea/Bay/Gulf | native | 5978 |
| Kaoping River | River (basin) | native | 36073 |
| Kuroshio Current | Sea/Bay/Gulf | native | 3424 |
| Lagonoy Gulf | Sea/Bay/Gulf | native | 43283 |
| Lake Mainit | Lake | native | 81829 |
| Leyte Gulf | Sea/Bay/Gulf | native | 31411 |
| Lingayen Gulf | Sea/Bay/Gulf | native | 43020 |
| Manila Bay | Sea/Bay/Gulf | native | 30919 |
| Mekong | River (basin) | native | 12693 |
| Naujan Lake | Lake | native | 280 |
| North Australian Shelf | Sea/Bay/Gulf | native | 4959 |
| Northeast Australian Shelf | Sea/Bay/Gulf | native | 4959 |
| Northwest Australian Shelf | Sea/Bay/Gulf | native | 4959 |
| Oriental | Zoogeographic realm | native | 12693 |
| Ormoc Bay | Sea/Bay/Gulf | native | 45140 |
| Pacific Ocean | Sea/Bay/Gulf | native | 6192 |
| 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 | 11441 |
| Ragay Gulf | Sea/Bay/Gulf | native | 47919 |
| Red Sea | Sea/Bay/Gulf | native | 84159 |
| Ruerhmen River | River (basin) | native | 36073 |
| Samar Sea | Sea/Bay/Gulf | native | 29039 |
| San Miguel Bay | Sea/Bay/Gulf | native | 43275 |
| San Pedro Bay | Sea/Bay/Gulf | native | 46240 |
| 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 | 12484 |
| 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 | 2858 |
| Taal Lake | Lake | native | 280 |
| Tayabas Bay | Sea/Bay/Gulf | native | 47573 |
| Tsengwen River | River (basin) | native | 36073 |
| Verde Island Passage | Sea/Bay/Gulf | native | 6956 |
| Visayan Sea | Sea/Bay/Gulf | native | 3557 |
| Yellow Sea | Sea/Bay/Gulf | native | 4868 |
| Zambezi | River (basin) | native | 39494 |