The San Juan River is an important water resource to residents of Navajo Nation and surrounding communities in the Four Corners Region of the southwestern USA. The primary uses of the San Juan River are agricultural, industrial, municipal, domestic, and stock watering. The Navajo Nation Environmental Protection Agency (NNEPA) identified elevated concentrations of aluminum, arsenic, and lead in the San Juan River under high flow hydrologic regimes. The U.S. Geological Survey, in collaboration with NNEPA, is working to identify the geochemical signatures of water, sediments, and rocks from 34 tributaries and 12 sub-watersheds within a 235-mile reach of the San Juan River. Baseflow surface water samples were collected at 16 points on the San Juan River in February 2021. Tributaries to the river, including 28 ephemeral channels and five perennial channels (four of which are fed by agricultural return water) were sampled during the spring snowmelt and summer monsoons of 2021. Total water chemistry concentrations of aluminum, arsenic and lead in the San Juan River increased during snowmelt and monsoonal storms compared to the baseflow samples. In addition, elevated concentrations of these metals are observed in some tributaries and appear to influence the concentration of those elements in the San Juan River. For comparison, in some cases, the concentrations are above drinking water standards. Sources of these elements could be natural or anthropogenic. Evaluation of sediment and rock chemistry in each sub-watershed will help to elucidate the potential source and/or mechanism of metal mobilization. Scanning electron microscopy on tributary sediments revealed minerals in the watershed, including barite, apatite, Fe-oxides, monazite, magnetite, framboidal pyrite, and ilmenite, that could be associated with one or more of the elements of interest. Determining the relative contribution and effect of each source to the San Juan River will help the Navajo Nation, public drinking-water managers, irrigation districts, scientists, and the public in their efforts to protect the environment and human health.