It is widely accepted that climate change is the main factor behind the accelerated glacier retreat observed in the Himalayas. The Eastern Himalayas have the largest concentration of glaciers outside the polar region, and hold vast stores of fresh water. Continued climate change is predicted to lead to major changes in freshwater flows, with dramatic impacts on biodiversity, people and their livelihoods.

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Conversion of forest to agriculture land and for development purposes, and the exploitation of forests for timber, fodder and fuel wood are some of the main threats to biodiversity in this region. Other threats include wood-charcoal production and intensive grazing. Many rural people depend on cattle for their livelihoods but do not have sufficient land holdings. It is not uncommon to see cows, water buffalo and goats grazing in forests, which can cause significant damage to natural ecosystems.

Poaching is a major threat to wildlife in the region, especially endangered species like tigers, elephants and rhinos, which have a high commercial value on the black market. Killing wildlife also takes place as a result of human-wildlife conflict. Retaliation against tigers and snow leopards for killing livestock, and against elephants and rhinoceros for raiding crops, is prevalent and continues to intensify as humans and wildlife compete for land and other resources.