The U.S. Geological Survey, in cooperation with the Missouri Department of Natural Resources, collected water and streambedsediment samples in the Upper Elk River Basin in southwestern Missouri and northwestern Arkansas from October 2004 through December 2006. The samples were collected to determine the stream-water quality and streambed-sediment quality. In 1998, the Missouri Department of Natural Resources included a 21.5-mile river reach of the Elk River on the 303(d) list of impaired waters in Missouri as required by Section 303(d) of the Federal Clean Water Act. The Elk River is on the 303(d) list for excess nutrient loading. The total phosphorus distribution by decade indicates that the concentrations since 2000 have increased significantly from those in the 1960s, 1980s, and 1990s. The nitrate as nitrogen (nitrate) concentrations also have increased significantly in post-1985 from pre-1985 samples collected at the Elk River near Tiff City. Concentrations have increased significantly since the 1960s. Concentrations in the 1970s and 1980s, though similar, have increased from those in the 1960s, and the concentrations from the 1990s and 2000s increased still more. Nitrate concentrations significantly increased in samples that were collected during large discharges (greater than 355 cubic feet per second) from the Elk River near Tiff City. Nitrate concentrations were largest in Indian Creek. Several sources of nitrate are present in the basin, including poultry facilities in the upper part of the basin, effluent inflow from communities of Anderson and Lanagan, land-applied animal waste, chemical fertilizer, and possible leaking septic systems. Total phosphorus concentrations were largest in Little Sugar Creek. The median concentration of total phosphorus from samples from Little Sugar Creek near Pineville was almost four times the median concentration in samples from the Elk River near Tiff City. Median concentrations of nutrient species were greater in the stormwater samples than the median concentrations in the ambient samples. Nitrate concentrations in stormwater samples ranged from 133 to 179 percent of the concentration in the ambient samples. The total phosphorus concentrations in the stormwater samples ranged from about 200 to more than 600 percent of the concentration in the ambient samples. Base-flow conditions as reflected by the seepage run of the summer of 2006 indicate that 52 percent of the discharge at the Elk River near Tiff City is contributed by Indian Creek. Little Sugar Creek contributes 32 percent and Big Sugar Creek 9 percent of the discharge in the Elk River near Tiff City. Only about 7 percent of the discharge at Tiff City comes from the mainstem of the Elk River. Concentrations of dissolved ammonia plus organic nitrogen as nitrogen, dissolved ammonia as nitrogen, dissolved phosphorus, and dissolved orthophosphorus were detected in all streambed-sediment leachate samples. Concentrations of leachable nutrients in streambed-sediment samples generally tended to be slightly larger along the major forks of the Elk River as compared to tributary sites, with sites in the upper reaches of the major forks having among the largest concentrations. Concentrations of leachable nutrients in the major forks generally decreased with increasing distance downstream.