Water-quality data from October 1969 to December 1999 for both surface water and ground water in the upper Gunnison River watershed were retrieved and compiled from the U.S. Geological Survey National Water Information System and the U.S. Environmental Protection Agency Storage and Retrieval databases. Analyses focused primarily on a subset of these data from October 1989 to December 1999. The upper Gunnison River watershed is located west of the Continental Divide in the Southern Rocky Mountains physiographic province.

Surface-water-quality data were compiled for 482 sites in the upper Gunnison River watershed. Most values of surface-water temperature, dissolved oxygen, and pH were within Colorado Department of Public Health and Environment (CDPHE) in-stream standards. Calcium bicarbonate type water was the most spatially dominant water type in the basin.

Nutrients were most commonly sampled along the Slate River and East River near Crested Butte and along the Gunnison River from the confluence of the East and Taylor Rivers to the western edge of the watershed. Median ammonia concentrations were low, with many concentrations less than laboratory reporting levels. All nitrate concentrations met the CDPHE in-stream standard of 10 milligrams per liter. More than 30 percent of stream sites with total phosphorus data (23 of 61 sites) had concentrations greater than the U.S. Environmental Protection Agency (USEPA) recommendation for controlling eutrophication.

Ammonia concentrations at a site on the Slate River near Crested Butte had a statistically significant upward trend for the 1995–99 period. The Slate River near Crested Butte site is located immediately downstream from the towns of Crested Butte and Mount Crested Butte and may reflect recent population growth or other land-use changes. However, the rate of change of the trend is small (0.017 milligram per liter per year).

Although a multiple comparison test showed nitrate concentrations were statistically different between agriculture and forest sites and between agriculture and urban land-use classified sites, median concentrations were low among all land-use settings. Median concentrations of total phosphorus were greatest in rangeland areas and least in urban areas. No significant differences were identified for median concentrations of total phosphorus in agriculture and forest land-use areas.

Median concentrations of arsenic, lead, mercury, selenium, and silver were low or below reporting levels throughout the watershed. Aluminum, cadmium, copper, lead, manganese, and zinc concentrations were elevated near the town of Crested Butte and on Henson Creek upstream from Lake City, which may be explained by upstream areas of historical mining. Samples for six trace elements exceeded standards: cadmium, copper, lead, manganese, silver, and zinc. A downward trend (3 micrograms per liter per year) was identified for the dissolved iron concentration at a site on the Gunnison River at County Road 32 downstream from the city of Gunnison. Streambed-sediment samples from areas affected by historical mining also had elevated concentrations of some trace elements.

Chlorophyll-a concentrations in samples from Blue Mesa Reservoir and streams in the Crested Butte and Gunnison areas were typical of unenriched to moderately enriched conditions. Median concentrations of 5-day biochemical oxygen demand concentrations for sites between Crested Butte and Blue Mesa Reservoir were less than 2 milligrams per liter. Occasional high (greater than 200 counts per 100 milliliters) concentrations for fecal coliform were determined at selected sites within the study area. However, median concentrations were less than 100 counts per 100 milliliters except for the Squaw Creek and Cimarron River areas in the western part of the watershed.

Ground-water-quality data have been collected by the U.S. Geological Survey from 99 wells. Many wells were completed in aquifers composed of Holocene-age valley fill and alluvium. Most field properties were within the USEPA Secondary Drinking Water Regulations (SDWR) range for treated drinking water, except for 2 (of 40) pH samples. Calcium bicarbonate was the predominant water type in nearly all aquifers except for the aquifers composed of volcanic rock, which had more sodium and sulfate mixed water types. Wells with sulfate concentrations exceeding the SDWR of 250 milligrams per liter were completed in aquifers composed of volcanic rock near Lake City. Dissolution and oxidation of sulfide minerals in these aquifers may explain the elevated sulfate concentrations in ground water at these locations.

Nutrient concentrations in ground water were generally low, and median concentrations for ammonia, nitrite, and dissolved phosphorus were below reporting levels. All nitrate concentrations in the samples were below the USEPA drinking-water maximum contaminant level of 10 mg/L. No statistical difference was found in nitrate concentrations among the four land-use classifications (agriculture, forest, rangeland, and urban).

Trace elements in ground water were generally below the USEPA SDWR. Three iron samples exceeded the USEPA SDWR of 300 micrograms per liter at two wells located near the city of Gunnison and at a well south of the town of Powderhorn near the Cebolla River. Nine of 39 manganese samples exceeded the USEPA SDWR of 50 micrograms per liter and were collected from aquifers composed of Holocene-age valley fill and alluvium near Gunnison and Crested Butte and in one well near the Cebolla River. Radon gas is a natural radioactive decay product of uranium. All 39 radon samples collected from ground water in the watershed exceeded the proposed USEPA drinking-water maximum contaminant level of 300 picocuries per liter and ranged from 426 to 3,830 picocuries per liter.