There are many international and local threats to the plants of Nepal. Globally, climate change is increasing temperatures and causing glaciers to retreat. Internationalisation of trade and agricultural practices is leading to a reduction in crop diversity, an increase in use of chemicals, and placing strain on wild populations through over-collection. Nationally, three root causes have been identified by the Nepal Biodiversity Strategy: socio-economic; natural; and anthropogenic.

• Widespread poverty and intimate dependence on almost all of the population on natural resources for their livelihood.
• Forests exploited as a major source of revenue until the late 1980’s.
• Fast population growth (2.23% in 2004)increasing demands for fuel, timber, fodder, grazing and agricultural land, leading to encroachment into natural ecosystems.
• Mass migration of people into the Terai and Dun valleys following malaria eradication in the mid 1950’s (see below under Terai), and refugee relocation from neighbouring countries.
• Increasing urbanisaton with migration rates from the countryside to urban areas in Nepal estimated at about 8% (the highest in South Asia), and the quality of life in the rapidly expanding major towns and cities is now suffering due to the added strain on sewerage, electricity and drinking water supplies, housing and vehicle pollution.

• Landslides in hilly regions (75% of landslides in Nepal occur naturally), especially during the monsoon (June-September) when the topsoil becomes saturated with water. All of Nepal's rivers flow across the Ganetic plain and drain into the Ganges, and so the floods that frequently devastate Nepal also bring disaster to India.
• Topsoil erosion, caused by natural and anthropogenic activities, leading to desertification and loss of soil fertility. The rat of soil loss for intact forested areas is estimated at below 1t/ha/yr, in degraded forest this increases to over 4t/ha/yr, and up to 200t/ha/yr in critically damaged areas.
   

• Pollution and environmental degradation, especially in urban and industrial areas.
• Infrastructure building projects implemented without consideration of environmental impact: e.g. roads, hydroelectric power stations, dams, irrigation channels, canals and quarries (marble, building stone, soils, etc.).
• Water supply has been affected by glacial retreat and contamination is a problem through human and animal waste, agricultural runoff and industrial effluents.
• Tourism and mountaineering expeditions in alpine areas (especially fuel wood needs of porters and support staff).
• Deforestation (past clearances for agriculture, and now mainly cutting for fuel wood) has led to severe environmental degradation and soil erosion.
• Fire, either deliberate or accidental, has profound effects on ecosystems, destroying forests and preventing re-growth. Fire may promote luxuriant growth of grasses in old pasture, but the timescale for forest regeneration is long.
• Overgrazing (especially by yaks and sheep) leading to an increase in unpalatable species, inhibition of ecological succession and promotion soil erosion.
• Alien species spread by increased human movement, out-compete native plants.
• Illegal trade and collection from wild sources (medicinal herbs, orchids and other horticultural plants).