While pristine by many standards, the health of the Crown of the Continent is threatened by the ramifications of global climate change. Plants and animals that have survived for thousands of years may face extirpation unless they can adapt to projected rising temperatures, changing precipitation, and an altering of the forces that have supported them for millennia. Human activities may also be at risk as climate-related changes affect water sources and other resources.

These climate changes are often more severe in mountain areas where species habitat can be narrow and fragmented. Research into alpine environments is aimed at obtaining a better understanding of how sensitive areas are responding to warming temperatures, melting alpine glaciers, altered water flow, shifting vegetation patterns, and a changing fire regime.