A five-year record of streamflow and chemical sampling data was evaluated to assess the effects of large-scale prairie restoration on transport of NO3-N, Cl, and SO4 loads from paired 5000-ha watersheds located in Jasper County, Iowa. Water quality conditions monitored during land use conversion from row crop agriculture to native prairie in the Walnut Creek watershed were compared with a highly agricultural control watershed (Squaw Creek). Combining hydrograph separation with a load estimation program, baseflow and stormflow loads of NO3-N, Cl, and SO4 were estimated at upstream and downstream sites on Walnut Creek and a downstream site on Squaw Creek. Chemical export in both watersheds was found to occur primarily with baseflow, with baseflow transport greatest during the late summer and fall. Lower Walnut Creek watershed, which contained the restored prairie areas, exported less NO3-N and Cl compared with upper Walnut Creek and Squaw Creek watersheds. Average flow-weighted concentrations of NO3-N exceeded 10 mg/L in upper Walnut Creek and Squaw Creek, but were estimated to be 6.6 mg/L in lower Walnut Creek. Study results demonstrate the utility of partitioning loads into baseflow and stormflow components to identify sources of pollutant loading to streams.