Although about 90 percent of the river's water originates as snowmelt in the Rocky Mountains of Colorado, the largest portion of the watershed – , or 40 percent – lies in New Mexico. A further 23 percent of the watershed is in Colorado, 20 percent is in Arizona, and 17 percent is in Utah. In terms of area drained, the Chaco River is the largest tributary draining , followed by Chinle Creek which drains . The Animas River is the largest tributary in terms of stream flow, but drains a comparatively slim watershed of . In the 21st century, the snowpack in the San Juan Mountains has often been diminished by warming winter temperatures which has led to concerns about the long-term water supply for the San Juan River. In addition, the mountains are particularly vulnerable to dust storms originating from the Great Basin; dust settling on snowpack increases the absorption of solar energy and often leads to premature melting.