| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Agulhas Current | Sea/Bay/Gulf | native | 7248 |
| Arabian Sea | Sea/Bay/Gulf | native | 4832 |
| Australian | Zoogeographic realm | native | 5259 |
| Bay of Bengal | Sea/Bay/Gulf | native | 41236 |
| Cauvery | River (basin) | native | 43636 |
| Chilika Lake/Lagoon | Lagoon | native | 29108 |
| Ethiopian | Zoogeographic realm | native | 3506 |
| Fitzroy | River (basin) | native | 84364 |
| Gulf of Aden | Sea/Bay/Gulf | native | 129076 |
| Indian Ocean | Sea/Bay/Gulf | native | 5259 |
| Indonesian Sea | Sea/Bay/Gulf | native | 7050 |
| Mekong | River (basin) | native | 12693 |
| North Australian Shelf | Sea/Bay/Gulf | native | 5259 |
| Oriental | Zoogeographic realm | native | 4832 |
| Pacific Ocean | Sea/Bay/Gulf | native | 5259 |
| Sabaki | River (basin) | native | 30558 |
| South China Sea | Sea/Bay/Gulf | native | 5193 |
| Tana | River (basin) | native | 32384 |
| Zambezi | River (basin) | native | 39494 |