Twenty-five years of groundwater quality monitoring in a sandy aquifer beneath agricultural fields showed large temporal and spatial variations in major ion groundwater chemistry, which were linked closely to the nitrate (NO₃) content of agricultural recharge. Between 1988 and 2013, the NO₃ content of water in the oxidized zone of the aquifer nearly halved, following implementation of action plans to reduce N leaching from agriculture. However, due to denitrification by pyrite oxidation in the aquifer, a plume of sulfate-rich water migrates through the aquifer as a legacy of the historical NO₃ loading. Agriculture thus is an important determinant of major ion groundwater chemistry. Temporal and spatial variations in the groundwater quality were simulated using a 2D reactive transport model, which combined effects of the historical NO₃ leaching and denitrification, with dispersive mixing into the pristine groundwater residing deeper in the aquifer. Reactant-to-product ratios across reaction fronts are altered by dispersive mixing and transience in reactant input functions. Modelling therefore allowed a direct comparison of observed and simulated ratios of concentrations of NO₃ (reactant) in the oxidized zone to those of SO₄ (product) in the reduced zone, which aided a stoichiometric assessment of the mechanisms of denitrification. Denitrification by pyrite in the Rabis Creek aquifer results in oxidation of S⁻¹ and Fe²⁺ in pyrite to S⁶⁺ in dissolved SO₄ and Fe³⁺ in Fe-oxide. Neither precipitation of elemental sulfur (S⁰), nor of jarosite, was supported by observations, and adsorption of sulfate was also dismissed.