The bioremediation of organic contaminants in the subsurface is strongly influenced by the existing geochemical environment. In this study a coupled reactive transport and geochemical model is developed for the simulation of enhanced bioremediation of organic contamination in the presence of pyrite. The two-dimensional model allows for the simulation of both kinetically defined as well as geochemical equilibrium reactions. The model is applied to a hypothetical pyrite-containing aquifer contaminated with petroleum hydrocarbons. Oxygen injected into the aquifer to enhance contaminant biodegradation reacts with pyrite resulting in reduced oxygen availability, acidification of the subsurface environment and, subsequently, the inadvertent inhibition of the microbial activity. The reactive transport and geochemical model is used to quantify these processes. The dominance of the various chemical reactions and the sensitivity of the biodegradation on pyrite content are evaluated. Through groundwater pH manipulation, the interference of pyrite with the intended remedial action is partially mitigated. It is shown that when oxygen availability is a limiting factor, the optimal pH that would maximize hydrocarbon degradation may significantly differ from the pH value that maximizes bacterial activity.