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Manure is applied to cropland areas managed under diverse conditions, resulting in varying amounts of residue cover. The objective of this study was to measure the effects of crop residue on nutrient concentrations in runoff from areas where beef cattle or swine manure were recently applied but not incorporated. Plots 0.75 m wide by 2 m long were established at the study site. Existing residue materials were removed, and corn, soybean, or winter wheat residue was added at rates of 2, 4, or 8 Mg ha−1. Manure was then applied at rates required to meet estimated annual nitrogen requirements for corn. Control plots with manure but no residue, and plots with no residue and no manure were also established. Three 30 min simulated rainfall events, separated by 24 h intervals, were conducted at an intensity of approximately 70 mm h−1. Dissolved phosphorus (DP), total phosphorus (TP), NO3−N, NH4−N, total nitrogen, runoff, and soil loss were measured for each rainfall event. When beef cattle or swine manure was applied to plots containing residue materials, nutrient concentrations in runoff were not affected by the amount of crop residue on the soil surface. Concentrations of DP and NO3−N in runoff from the plots with beef cattle manure were significantly greater on the plots with residue than on the no-residue treatments. No significant differences in runoff nutrient concentrations were found between the residue and no-residue treatments with swine manure. Concentrations of DP and TP were significantly less on the no-residue/no-manure treatment than on the plots with beef cattle or swine manure.