Water-quality and ecological character and trends in the metropolitan Blue River Basin were evaluated from 1998 through 2007 to provide spatial and temporal resolution to factors that affect the quality of water and biota in the basin and provide a basis for assessing the efficacy of long-term combined sewer control and basin management plans. Assessments included measurements of stream discharge, pH, dissolved oxygen, specific conductance, turbidity, nutrients (dissolved and total nitrogen and phosphorus species), fecal-indicator bacteria (Escherichia coli and fecal coliform), suspended sediment, organic wastewater and pharmaceutical compounds, and sources of these compounds as well as the quality of stream biota in the basin. Because of the nature and myriad of factors that affect basin water quality, multiple strategies are needed to decrease constituent loads in streams. Strategies designed to decrease or eliminate combined sewer overflows (CSOs) would substantially reduce the annual loads of nutrients and fecal-indicator bacteria in Brush Creek, but have little effect on Blue River loadings. Nonpoint source reductions to Brush Creek could potentially have an equivalent, if not greater, effect on water quality than would CSO reductions. Nonpoint source reductions could also substantially decrease annual nutrient and bacteria loadings to the Blue River and Indian Creek. Methods designed to decrease nutrient loads originating from Blue River and Indian Creek wastewater treatment plants (WWTPs) could substantially reduce the overall nutrient load in these streams. For the main stem of the Blue River and Indian Creek, primary sources of nutrients were nonpoint source runoff and WWTPs discharges; however, the relative contribution of each source varied depending on how wet or dry the year was and the number of upstream WWTPs. On Brush Creek, approximately two-thirds of the nutrients originated from nonpoint sources and the remainder from CSOs. Nutrient assimilation processes, which reduced total nitrogen loads by approximately 13 percent and total phosphorus loads by double that amount in a 20-kilometer reach of the Blue River during three synoptic base-flow sampling events between August through September 2004 and September 2005, likely are limited to selected periods during any given year and may not substantially reduce annual nutrient loads. Bacteria densities typically increased with increasing urbanization, and bacteria loadings to the Blue River and Indian Creek were almost entirely the result of nonpoint source runoff. WWTPs contributed, on average, less than 1 percent of the bacteria to these reaches, and in areas of the Blue River that had combined sewers, CSOs contributed only minor amounts (less than 2 percent) of the total annual load in 2005. The bulk of the fecal-indicator bacteria load in Brush Creek also originated from nonpoint sources with the remainder from CSOs. From October 2002 through September 2007, estimated daily mean Escherichia coli bacteria density in upper reaches of the Blue River met the State of Missouri secondary contact criterion standard approximately 85 percent of the time. However, in lower Blue River reaches, the same threshold was exceeded approximately 45 percent of the time. The tributary with the greatest number of CSO discharge points, Brush Creek, contributed approximately 10 percent of the bacteria loads to downstream reaches. The tributary Town Fork Creek had median base-flow Escherichia coli densities that were double that of other basin sites and stormflow densities 10 times greater than those in other parts of the basin largely because approximately one-fourth of the runoff in the Town Fork Creek Basin is believed to originate in combined sewers. Genotypic source typing of bacteria indicated that more than half of the bacteria in this tributary originated from human sources with two storms contributing the bulk of all bacteria sourced as human. However, areas outsid