Artificial recharge is a technique used increasingly to supplement drinking water supplies. To assess the potential water quality changes that occur during subsurface passage, a comprehensive deep-well injection experiment was carried out for a recharge scheme, where pretreated, aerobic surface water was injected at 300 m depth into an anaerobic aquifer. Water quality parameters were recorded over the 854-days long injection phase. The evolution of the major ion and redox chemistry was analyzed with a three-dimensional reactive multicomponent transport model. It was found that the oxidation of pyrite was the main driver for water quality changes and that reaction rates depended significantly on the spatially/temporally varying groundwater temperature. With the temperature-dependency of the oxidation reactions incorporated into the model, the simulations give an accurate picture of the temporal and spatial evolution of the hydrochemical changes that occurred during the experiment. To delineate the influence of physical and chemical processes on local concentration changes the results of the reactive transport model simulations were compared with the corresponding results from nonreactive simulations. The study emphasizes the suitability of mechanistic multicomponent reactive transport modeling as an integrative tool for data analysis when physical transport and chemical processes interact. © 2005 American Chemical Society.