Understanding how nitrogen fluxes respond to changes in agriculture and climate is important for improving water quality. In the midwestern USA, expansion of corn cropping for ethanol production led to increasing N application rates in the 2000s during a period of extreme variability of annual precipitation. To examine the effects of these changes, surface water quality was analyzed in 10 major Iowa Rivers. Several decades of concentration and flow data were analyzed with a statistical method that provides internally consistent estimates of the concentration history and reveals flow-normalized trends that are independent of year-to-year streamflow variations. Flow-normalized concentrations of nitrate+nitrite-N decreased from 2000 to 2012 in all basins. To evaluate effects of annual discharge and N loading on these trends, multiple conceptual models were developed and calibrated to flow-weighted annual concentrations. The recent declining concentration trends can be attributed to both very high and very low discharge in the 2000’s and to the long (e.g. 8-year) subsurface residence times in some basins. Dilution of N and depletion of stored N occurs in years with high discharge. Reduced N transport and increased N storage occurs in low-discharge years. Central Iowa basins showed the greatest reduction in flow-normalized concentrations, likely because of smaller storage volumes and shorter residence times. Effects of land-use changes on the water quality of major Iowa Rivers may not be noticeable for years or decades in peripheral basins of Iowa, and may be obscured in the central basins where extreme flows strongly affect annual concentration trends.