Livestock are a critical agricultural commodity in the Midwestern United States and are directly linked to row crop production. Chemical and manure nutrient application for row crop production has resulted in significant losses of nitrogen (N) and phosphorus (P) to downstream ecosystems causing environmental crises like seasonal hypoxia in the Gulf of Mexico. However, the use of cattle manure has multiple benefits over commercial fertilizer including increased soil carbon levels and improved nutrient cycling and should be considered a critical component for future agricultural production in Iowa. In this study, we evaluated influences of bedded cattle manure and commercial fertilizer on groundwater quality in a field with varying soil parent material of glacial till and colluvium in eastern Iowa. We found that soil parent material predominately influenced groundwater quality. Multiple water quality parameters including nitrate varied significantly (p < 0.0001). Nitrate concentrations were nearly double in colluvium compared to glacial till (13.2 ± 6.7 compared to 7.0 ± 3.6 mg/L, respectively). Further, nitrate concentrations averaged 12.2 ± 8.1 mg/L in areas receiving bedded cattle manure and were significantly higher (p < 0.0001) compared to areas receiving commercial fertilizer only, which averaged 8.6 ± 4.7 mg/L. Dissolved P was significantly lower (p < 0.05) in areas receiving bedded cattle manure averaging 0.13 ± 0.12 mg/L compared to 0.07 ± 0.04 mg/L in commercial fertilizer‐only areas. However, higher nitrate concentrations were likely linked to 70 kg/ha of additional N applied to manure areas by farm managers above corn removal rates. Overall, our results stress the importance of appropriate nutrient application rates and placement over nutrient source.