Trends in streamflow and concentration of total nitrogen, nitrite plus nitrate, ammonia, total phosphorus, orthophosphorus, and suspended sediment were determined for the period from 1993 to 2003 at selected stream sites in the Missouri River Basin. Flow-adjusted trends in concentration (the trends that would have occurred in the absence of natural changes in streamflow) and non-flow-adjusted trends in concentration (the overall trends resulting from natural and human factors) were determined. In the analysis of flow-adjusted trends, the removal of streamflow as a variable affecting concentration allowed trends caused by other factors such as implementation of best management practices to be identified. In the analysis of non-flow-adjusted trends, the inclusion of any and all factors affecting concentration allowed trends affecting aquatic ecosystems and the status of streams relative to water-quality standards to be identified. Relations between the flow-adjusted and non-flow-adjusted trends and changes in streamflow, nutrient sources, ground-water inputs, and implementation of management practices also were examined to determine the major factors affecting the trends. From 1993 to 2003, widespread downward trends in streamflow indicated that drought conditions from about 2000 to 2003 led to decreasing streamflow throughout much of the Missouri River Basin. Flow-adjusted trends in nitrite plus nitrate and ammonia concentrations were split nearly equally between nonsignificant and downward; at about one-half of the sites, management practices likely were contributing to measurable decreases in concentrations of nitrite plus nitrate and ammonia. Management practices had less of an effect on concentrations of total nitrogen; downward flow-adjusted trends in total nitrogen concentrations occurred at only 2 of 19 sites. The pattern of non-flow-adjusted trends in nitrite plus nitrate concentrations was similar to the pattern of flow-adjusted trends; non-flow-adjusted trends were split nearly equally between nonsignificant and downward. A substantial source of nitrite plus nitrate to these streams likely was ground water; because of the time required for ground water to travel to streams, there may have been a lag time between the implementation of some pollution-control strategies and improvement in stream quality, contributing to the nonsignificant trends in nitrite plus nitrate. There were more sites with downward non-flow-adjusted trends than flow-adjusted trends in both ammonia and total nitrogen concentrations, possibly a result of decreased surface runoff from nonpoint sources associated with the downward trends in streamflow. No strong relations between any of the nitrogen trends and changes in nutrient sources or landscape characteristics were identified. Although there were very few upward trends in nitrogen from 1993 to 2003, there were upward flow-adjusted trends in total phosphorus concentrations at nearly one-half of the sites. At these sites, not only were pollution-control strategies not contributing to measurable decreases in total phosphorus concentrations, there was likely an increase in phosphorus loading on the land surface. There were fewer upward non-flow-adjusted than flow-adjusted trends in total phosphorus concentrations; at the majority of sites, overall total phosphorus concentrations did not change significantly during this period. The preponderance of upward flow-adjusted trends and nonsignificant non-flow-adjusted trends indicates that in some areas of the Missouri River Basin, overall concentrations of total phosphorus would have been higher without the decrease in streamflow and the associated decrease in surface runoff during the study period. During the study period, phosphorus loads from fertilizer generally increased at over one-half of the sites in the basin. Upward flow-adjusted trends were related to increasing fertilizer use in the upstream drainage area, particularly in the 10 percent