The water-quality reconnaissance of the San Rafael River basin, Utah, encompassed an area of about 2,300 square miles (5,960 square kilometers). Data were obtained by the U.S. Geological Survey one or more times at 116 sites from June 1977 to September 1978. At 19 other sites visited during the same period, the streams were dry. Precipitation and stream discharge were significantly less than normal during 1977 and ranged from less than to more than normal during 1978. Exposed rocks in the San Rafael River basin range in age from Permian to Holocene. The Carmel Formation of Jurassic age and various members of the Mancos Shale of Cretaceous age are major contributors of dissolved solids to streams in the basin. There are eight major reservoirs having a total usable capacity of 115, 000 acre-feet (142 cubic hectometers); seven are mainly for irrigation supply; one, having a usable capacity of 30,530 acre-feet (38 cubic hectometers), is for power plant water supply. From about April to November, major diversions from Huntington, Cottonwood, and Ferron Creeks nearly deplete the flow downstream; during such periods, downstream flow in these streams and in the San Rafael River is mainly irrigation-return flow and some ground-water seepage. The water at the points of major diversion on Huntington, Cottonwood, and Ferron Creeks is of excellent quality for irrigation; salinity hazard is low to medium, and sodium hazard is low. Dissolved-solids concentrations are less than 500 milligrams per liter. The water at the mouths of Huntington, Cottonwood, and Ferron Creeks has markedly larger dissolved-solids concentrations than does the water upstream from major diversions. The changes in the chemical quality occur in stream reaches that cross a belt of land 10 to 15 miles (16 to 24 kilometers) wide where the Mancos Shale is widely exposed. This also is the area where nearly all the intensive irrigation in the San Rafael River basin is practiced. There are no perennial tributaries to the San Rafael River downstream from Ferron Creek. Except during infrequent short periods of runoff from cloudbursts or snowmelt, the flow in the San Rafael River is composed of the flow that reaches the mouths of Huntington, Cottonwood, and Ferron Creeks. The quality of water in the mainstem of the San Rafael River is largely determined by the major consumptive use of water for irrigation in upstream areas and by the poor quality of irrigation-return flow. During the data-collection periods for this study, dissolved-solids concentrations in the San Rafael River were more than 2,000 milligrams per liter except during snowmelt runoff in June 1978 and during a major flood in August 1977. The concentrations of trace elements, with the exception of strontium, were relatively small; strontium concentrations exceeded 1,500 micrograms per liter at seven sites. Most of the suspended-sediment discharge of the San Rafael River probably occurs during a few days each year and results mainly from cloudburst runoff.