Abstract: The Crown of the Continent is one of the premiere ecosystems in North America containing Waterton-Glacier International Peace Park, the Bob Marshall-Great Bear-Scapegoat Wilderness Complex in Montana, various Provincial Parks in British Columbia and Alberta, several national and state forest lands in the USA, and Crown Lands in Canada. The region is also the headwater source for three of the continent’s great rivers: Columbia, Missouri and Saskatchewan that flow to the Pacific, Atlantic and Arctic Oceans, respectively. Headwaters originate in high elevation alpine environs characterized by high snow accumulations in winter and rainstorms in summer. Most headwaters of the region contain high quality waters with few ions in solution and extremely low nutrient concentrations. Alpine streams have few species of aquatic organisms; however, they often possess rare species and have hydrogeomorphic features that make them vulnerable to climatic change. Subalpine and valley bottom streams of the Crown of the Continent Ecosystem (CCE) flow through well forested watersheds. Along the elevation gradient, the streams and rivers of the CCE flow through series of confining and nonconfining valleys resulting in distinct canyon and floodplain reaches. The alluvial floodplains are characterized by high species diversity and bioproduction maintained by the hydrologic linkages of habitats. The streams and rivers of the CCE have low nutrient concentrations, but may be significantly affected by wildfire, various resource extraction activities, such as logging or mining and exurban encroachment. Wildfire has been shown to increase nutrient loading in streams, both during a fire and then following the fire for as much as 5 years. Logging practices increase nutrient loading and the algal productivity of stream periphyton. Logging and associated roads are also known to increase sediment transport into Crown of the Continent streams directly affecting spawning success of native trout. The CCE is one of the fastest growing regions in the USA because of the many recreational amenities of the region. And, while the region has many remarkably pristine headwater streams and receiving rivers, there are many pending threats to water quality and quantity. One of the most urgent threats comes from the coal and gas fields in the northern part of the Crown of the Continent, where coal deposits are proposed for mountain-top removal and open-pit mining operations. This will have significant effects on the waters of the region, its native plants and animals and quality of life of the people.