Nitrate (NO3--N) contamination of groundwater and associated surface waters is an increasingly important global issue with multiple impacts on terrestrial, aquatic and atmospheric environments. Investigation of the distribution of hydrogeochemical variables and their connection with the occurrence of NO3--N provides better insights into the prediction of the environmental risk associated with nitrogen use within agricultural systems. The research objective was to evaluate the effect of hydrogeological setting on agriculturally derived groundwater NO3--N occurrence. Piezometers (n = 36) were installed at three depths across four contrasting agricultural research sites. Groundwater was sampled monthly for chemistry and dissolved gases, between February 2009 and January 2011. Mean groundwater NO3--N ranged 0.7-14.6 mg L-1, with site and groundwater depth being statistically significant (p<0.001). Unsaturated zone thickness and saturated hydraulic conductivity (K-sat) were significantly correlated with dissolved oxygen (DO) and redox potential (Eh) across sites. Groundwater NO3--N occurrence was significantly negatively related to DOC and methane and positively related with Eh and K-sat. Reduction of NO3--N started at Eh potentials <150 mV while significant nitrate reduction occurred <100 mV. Indications of heterotrophic and autotrophic denitrification were observed through elevated dissolved organic carbon (DOC) and oxidation of metal bound sulphur, as indicated by sulphate (SO42-). Land application of waste water created denitrification hot spots due to high DOC losses. Hydrogeological settings significantly influenced groundwater nitrate occurrence and suggested denitrification as the main control.