The National Water-Quality Assessment Program of the U.S. Geological Survey initiated an assessment in 1997 of the quality of water resources in the Yellowstone River Basin. Water-quality samples regularly were collected during 1999-2001 at 10 fixed sites on streams representing the major environmental settings of the basin. Integrator sites, which are heterogeneous in land use and geology, were established on the mainstem of the Yellowstone River (4 sites) and on three major tributaries?Clarks Fork Yellowstone River (1 site), the Bighorn River (1 site), and the Powder River (1 site). Indicator sites, which are more homogeneous in land use and geology than the integrator sites, were located on minor tributaries with important environmental settings?Soda Butte Creek in a mineral resource area (1 site), the Tongue River in a forested area (1 site), and the Little Powder River in a rangeland area (1 site). Water-quality sampling frequency generally was at least monthly and included field measurements and laboratory analyses of fecal-indicator bacteria, major ions, dissolved solids, nutrients, trace elements, pesticides, and suspended sediment. Median concentrations of fecal coliform and Escherichia coli were largest for basins that were predominantly rangeland and smallest for basins that were predominantly forested. Concentrations of fecal coliform and Escherichia coli significantly varied by season (p-value <0.001); the smallest median concentrations were during January?March and the largest median concentrations were during April?June. Fecal-coliform concentrations exceeded the U.S. Environmental Protection Agency recommended limit for a single sample of 400 colonies per 100 milliliters in 2.6 percent of all samples. Escherichia coli concentrations exceeded the U.S. Environmental Protection Agency recommended limit for a single sample of 298 colonies per 100 milliliters for moderate use, full-body contact recreation in 7.6 percent of all samples. Variations in water type in the basin are reflective of the diverse geologic terrain in the Yellowstone River Basin. The water type of Soda Butte Creek and the Tongue River was calcium bicarbonate. These two sites are in forested and mountainous areas where igneous rocks and Paleozoic-era and Mesozoic-era sedimentary rocks are the dominant geologic groups. The water type of the Little Powder River was sodium sulfate. The Little Powder River originates in the plains, and geology of the basin is nearly homogenous with Tertiary-period sedimentary rocks. Water type of the Yellowstone River changed from a mixed-cation bicarbonate type upstream to a mixed-cation sulfate type downstream. Dissolved-solids concentrations ranged from fairly dilute in Soda Butte Creek, which had a median concentration of 118 milligrams per liter, to concentrated in the Little Powder River, which had a median concentration of 2,840 milligrams per liter. Nutrient concentrations generally were small and reflect the relatively undeveloped conditions in the basin; however, some correlations were made with anthropogenic factors. Median dissolved-nitrate concentrations in all samples from the fixed sites ranged from 0.04 milligram per liter to 0.54 milligram per liter. Flow-weighted mean dissolved-nitrate concentrations were positively correlated with increasing agricultural land use and rangeland on alluvial deposits upstream from the sites and negatively correlated with increasing forested land. Ammonia concentrations generally were largest in samples collected from the Yellowstone River at Corwin Springs, Montana, which is downstream from Yellowstone National Park and receives discharge from geothermal waters that are high in ammonia. Median total-phosphorus concentrations ranged from 0.007 to 0.18 milligram per liter. Median total-phosphorus concentrations exceeded the U.S. Environmental Protection Agency's recommended goal of 0.10 milligram per liter for preventing nuisance plant growth for samples collec