| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Adma River | River (basin) | native | 89719 |
| Bagmati | River (basin) | native | 40948 |
| Bhimtal Lake | Lake | native | 89721 |
| Brahmaputra | River (basin) | native | 89719 |
| Ganges | River (basin) | native | 4832 |
| Gaylegphug | River (basin) | native | 40882 |
| Jayanti River | River (basin) | native | 89719 |
| Kali Gandaki | River (basin) | native | 40948 |
| Kosi | River (basin) | native | 40948 |
| Manas | River (basin) | native | 40882 |
| Nainital Lake | Lake | native | 89721 |
| Naukuchiatal Lake | Lake | native | 89721 |
| Oriental | Zoogeographic realm | endemic | 31807 |
| Salween | River (basin) | native | 26580 |
| Sarbhang Khola | River (basin) | native | 40882 |