| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Arabian Sea | Sea/Bay/Gulf | native | 4832 |
| Bay of Bengal | Sea/Bay/Gulf | native | 5736 |
| Cauvery | River (basin) | native | 43636 |
| Chilika Lake/Lagoon | Lagoon | native | 29108 |
| Indian Ocean | Sea/Bay/Gulf | native | 4832 |
| Krishna River | River (basin) | native | 43636 |
| Lake Lanao | Lake | native | 13446 |
| Lake Mainit | Lake | native | 13446 |
| Naujan Lake | Lake | native | 13446 |
| Oriental | Zoogeographic realm | endemic | 4832 |
| Taal Lake | Lake | native | 13446 |