| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Adma River | River (basin) | native | 89719 |
| Bagmati | River (basin) | native | 40948 |
| Buxa River | River (basin) | native | 89719 |
| Indus | River (basin) | native | 41033 |
| Jayanti River | River (basin) | native | 89719 |
| Kali Gandaki | River (basin) | native | 40948 |
| Karnali | River (basin) | native | 40948 |
| Kosi | River (basin) | native | 40948 |
| Nainital Lake | Lake | native | 89721 |
| Oriental | Zoogeographic realm | endemic | 12076 |
| Sankosh | River (basin) | native | 40882 |
| Sarbhang Khola | River (basin) | native | 40882 |