| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Adma River | River (basin) | native | 89719 |
| Bhimtal Lake | Lake | native | 89721 |
| Brahmaputra | River (basin) | native | 121779 |
| Cauvery | River (basin) | native | 43636 |
| Chao Phraya River | River (basin) | native | 26580 |
| Chilika Lake/Lagoon | Lagoon | native | 29108 |
| Chittar River | River (basin) | native | 44312 |
| Choto Jamuna | River (basin) | native | 100698 |
| Ganges | River (basin) | native | 121779 |
| Gaylegphug | River (basin) | native | 40882 |
| Godavari | River (basin) | native | 43636 |
| Indus | River (basin) | native | 41033 |
| Irrawaddy | River (basin) | native | 43281 |
| Jayanti River | River (basin) | native | 89719 |
| Kabul | River (basin) | native | 41033 |
| Kali Gandaki | River (basin) | native | 40948 |
| Karnali | River (basin) | native | 40948 |
| Kosi | River (basin) | native | 40948 |
| Krishna River | River (basin) | native | 43636 |
| Mekong | River (basin) | native | 26336 |
| Nainital Lake | Lake | native | 89721 |
| Naukuchiatal Lake | Lake | native | 89721 |
| Oriental | Zoogeographic realm | endemic | 12076 |
| Salween | River (basin) | native | 26336 |
| Sarbhang Khola | River (basin) | native | 40882 |