| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Bhimtal Lake | Lake | native | 89721 |
| Ganges | River (basin) | native | 41236 |
| Kali Gandaki | River (basin) | native | 40948 |
| Karnali | River (basin) | native | 40948 |
| Kosi | River (basin) | native | 40948 |
| Nainital Lake | Lake | native | 89721 |
| Naukuchiatal Lake | Lake | native | 89721 |
| Oriental | Zoogeographic realm | endemic | 4832 |