This paper describes the modeling of the hydrogeochemical effects of deep well recharge of oxic water into an anoxic pyrite-bearing aquifer. Kinetic expressions have been used for mineral dissolution-precipitation rates and organic matter oxidation. Hydrological and chemical parameters of the model were calibrated to field measurements. The results showed that oxidation of pyrite (FeS(2)) and, to a lesser extent, organic matter dominate the changes in quality of the recharged water during its passage through the aquifer. The recharge leads to the consumption of oxygen and nitrate and the formation of sulfate and ferrihydrite. Complexation reactions, cation exchange and precipitation and dissolution of calcite, siderite and rhodochrosite were also identified through the modeling. Despite problems of non-uniqueness of the calibrated parameters, the model was used successfully to depict the geochemical processes occurring in the aquifer. Non-uniqueness can be avoided by constraining the model as much as possible to measurements and/or data from literature, although they cannot be considered always as fixed values and should be considered as stochastic variables instead.