Long-term changes in nitrate concentration and flux between the middle of the 20th century and the first decade of the 21st century were estimated for the Des Moines River and the Middle Illinois River, two Midwestern Corn Belt streams, using a novel weighted regression approach that is able to detect subtle changes in solute transport behavior over time. The results show that the largest changes in flow-normalized concentration and flux occurred between 1960 and 1980 in both streams, with smaller or negligible changes between 1980 and 2004. Contrasting patterns were observed between (1) nitrate export linked to non-point sources, explicitly runoff of synthetic fertilizer or other surface sources and (2) nitrate export presumably associated with point sources such as urban wastewater or confined livestock feeding facilities, with each of these modes of transport important under different domains of streamflow. Surface runoff was estimated to be consistently most important under high-flow conditions during the spring in both rivers. Nitrate export may also have been considerable in the Des Moines River even under some conditions during the winter when flows are generally lower, suggesting the influence of point sources during this time. Similar results were shown for the Middle Illinois River, which is subject to significant influence of wastewater from the Chicago area, where elevated nitrate concentrations were associated with at the lowest flows during the winter and fall. By modeling concentration directly, this study highlights the complex relationship between concentration and streamflow that has evolved in these two basins over the last 50 years. This approach provides insights about changing conditions that only become observable when stationarity in the relationship between concentration and streamflow is not assumed.