| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Agulhas Current | Sea/Bay/Gulf | native | 5285 |
| Australian | Zoogeographic realm | native | 2847 |
| Bay of Bengal | Sea/Bay/Gulf | native | 1479 |
| Chilika Lake/Lagoon | Lagoon | native | 29108 |
| Ethiopian | Zoogeographic realm | native | 6802 |
| Gulf of Aden | Sea/Bay/Gulf | native | 117436 |
| Indian Ocean | Sea/Bay/Gulf | native | 6802 |
| Indonesian Sea | Sea/Bay/Gulf | native | 7050 |
| Kaoping River | River (basin) | native | 36073 |
| Lingayen Gulf | Sea/Bay/Gulf | native | 5399 |
| Mekong | River (basin) | native | 12693 |
| North Australian Shelf | Sea/Bay/Gulf | native | 30874 |
| Oriental | Zoogeographic realm | native | 1479 |
| Pacific Ocean | Sea/Bay/Gulf | native | 592 |
| Peng-hu Island | Sea/Bay/Gulf | native | 55073 |
| Ruerhmen River | River (basin) | native | 36073 |
| Sabaki | River (basin) | native | 30558 |
| Shihtsao River | River (basin) | native | 36073 |
| Shiliao River | River (basin) | native | 36073 |
| Somali Coastal Current | Sea/Bay/Gulf | native | 30558 |
| South China Sea | Sea/Bay/Gulf | native | 36648 |
| Southern China | Sea/Bay/Gulf | native | 94637 |
| Taal Lake | Lake | native | 80679 |
| Tahiti Basins | River (basin) | native | 12792 |
| Tana | River (basin) | native | 52331 |
| Tañon Strait | Sea/Bay/Gulf | native | 11337 |
| Verde Island Passage | Sea/Bay/Gulf | native | 6956 |