Effective management of existing water-storage capacity in the Arkansas River Basin is anticipated to help satisfy the need for water in southeastern Colorado. A strategy to meet these needs has been developed, but implementation could affect the water quality of the Arkansas River and Fountain Creek in the vicinity of Pueblo, Colorado. Because no known methods are available to determine what effects future changes in operations will have on water quality, the U.S. Geological Survey, in cooperation with the Southeastern Colorado Water Activity Enterprise, began a study in 2002 to develop methods that could identify if future water-quality conditions have changed significantly from background (preexisting) water-quality conditions. A method was developed to identify when significant departures from background (preexisting) water-quality conditions occur in the lower Arkansas River and Fountain Creek in the vicinity of Pueblo, Colorado. Additionally, the methods described in this report provide information that can be used by various water-resource agencies for an internet-based decision-support tool. Estimated dissolved-solids concentrations at five sites in the study area were evaluated to designate historical background conditions and to calculate tolerance limits used to identify statistical departures from background conditions. This method provided a tool that could be applied with defined statistical probabilities associated with specific tolerance limits. Drought data from 2002 were used to test the method. Dissolved-solids concentrations exceeded the tolerance limits at all four sites on the Arkansas River at some point during 2002. The number of exceedances was particularly evident when streamflow from Pueblo Reservoir was reduced, and return flows and ground-water influences to the river were more prevalent. No exceedances were observed at the site on Fountain Creek. These comparisons illustrated the need to adjust the concentration data to account for varying streamflow. As such, similar comparisons between flow-adjusted data were done. At the site Arkansas River near Avondale, nearly all the 2002 flow-adjusted concentration data were less than the flow-adjusted tolerance limit which illustrated the effects of using flow-adjusted concentrations. Numerous exceedances of the flow-adjusted tolerance limits, however, were observed at the sites Arkansas River above Pueblo and Arkansas River at Pueblo. These results indicated that the method was able to identify a change in the ratio of source waters under drought conditions. Additionally, tolerance limits were calculated for daily dissolved-solids load and evaluated in a similar manner. Several other mass-load approaches were presented to help identify long-term changes in water quality. These included comparisons of cumulative mass load at selected sites and comparisons of mass load contributed at the Arkansas River near Avondale site by measured and unmeasured sources.