| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Australian | Zoogeographic realm | native | 59012 |
| Bonaparte Coast | Sea/Bay/Gulf | native | 75154 |
| Central and Southern Great Barrier Reef | Sea/Bay/Gulf | native | 75154 |
| Chiku River | River (basin) | native | 36073 |
| Indian Ocean | Sea/Bay/Gulf | native | 559 |
| Indonesian Sea | Sea/Bay/Gulf | native | 7050 |
| Oriental | Zoogeographic realm | native | 559 |
| Pacific Ocean | Sea/Bay/Gulf | native | 7050 |
| Shihtsao River | River (basin) | native | 36073 |
| South China Sea | Sea/Bay/Gulf | native | 36648 |
| Torres Strait Northern Great Barrier Reef | Sea/Bay/Gulf | native | 75154 |
| Tsengwen River | River (basin) | native | 36073 |
| West Philippine Sea | Sea/Bay/Gulf | native | 118511 |