Water-quality data were collected from sites in the Blue River Basin from July 1998 to October. Sites upstream from wastewater-treatment plants or the combined sewer system area had lower concentrations of total nitrogen, phosphorus, organic wastewater compounds, and pharmaceuticals, and more diverse aquatic communities. Sites downstream from wastewater-treatment plants had the largest concentrations and loads of nutrients, organic wastewater compounds, and pharmaceuticals. Approximately 60 percent of the total nitrogen and phosphorus in Blue River originated from the Indian Creek, smaller amounts from the upper Blue River (from 28 to 16 percent), and less than 5 percent from Brush Creek. Nutrient yields from the Indian Creek and the middle Blue River were significantly greater than yields from the upper Blue River, lower Brush Creek, the outside control site, and other U.S. urban sites. Large concentrations of nutrients led to eutrophication of impounded Brush Creek reaches. Bottom sediment samples collected from impoundments generally had concentrations of organic wastewater and pharmaceutical compounds equivalent to or greater than, concentrations observed in streambed sediments downstream from wastewater-treatment plants. Bacteria in streams largely was the result of nonpoint-source contributions during storms. Based on genetic source-tracking, average contributions of in-stream Esherichia coli bacteria in the basin from dogs ranged from 26-32 percent of the total concentration, and human sources ranged from 28-42 percent. Macro invertebrate diversity was highest at sites with the largest percentage of upstream land use devoted to forests and grasslands. Declines in macro invertebrate community metrics were correlated strongly with increases in several, inter-related urbanization factors.