The unsaturated zone serves as reservoir for geogenic and anthropogenic contaminants to local groundwater. Biogeochemical processes in this zone can be affected by nitrogen and water infiltration mobilizing contaminants, ultimately affecting groundwater quality. In this large-scale study, we evaluated the effects of estimated water and nitrogen inputs to the unsaturated zone of a public water supply wellhead protection (WHP) area with respect to subsurface occurrence and transport of nitrate, ammonium, arsenic, and uranium. Thirty-two coring sites were sampled and grouped by water application volume, irrigated – sprinkler (n=20), gravity (n=4) and non-irrigated land use. Unsaturated zone sediments were evaluated for the potential to mobilize arsenic and uranium in relation to nitrogen and water use. Sediment nitrate and ammonium had strong significant (p<0.05) correlation under all water application. Nitrate concentrations were lower beneath sprinkler-irrigated sites but had statistically higher ammonium concentrations than gravity-irrigated. Sediment nitrate concentrations were significantly (p<0.05) different among water application types, suggesting a strong effect of water volume on the changing nitrate concentration. Sediment arsenic presumably attenuated by iron (r=0.32 p<0.05). Uranium in sediments of unsaturated zone was negatively correlated to increase in sediment nitrate (r=-0.23 p<0.05) and ammonium (r=-0.19 p<0.05). Water application types were found to significantly influence sediment arsenic and uranium. While the groundwater arsenic and uranium concentration were below maximum contaminant levels, the highest uranium concentrations were observed in samples from WHP area. The study suggests that irrigation has an impact on unsaturated zone geochemistry with the potential to ultimately affect groundwater quality.