A three-dimensional model for predicting redox controlled, multi-species reactive transport processes in groundwater systems is presented. The model equations were fully integrated within a MODFLOW-family reactive transport code, RT3D. The model can simulate organic compound biodegradation coupled to different terminal electron acceptor processes. A computational approach, which uses the spatial and temporal distribution of the rates of different redox reactions, is proposed to map redox zones. The method allows one to quantify and visualize the biological degradation reactions occurring in three distinct patterns involving fringe, pseudo-core and core processes. The capabilities of the numerical model are demonstrated using two hypothetical examples: a batch problem and a simplified two-dimensional reactive transport problem. The model is then applied to an unconfined aquifer underlying a leaking landfill located near the city of Turin, in Piedmont (Italy). At this site, high organic load from the landfill leachate activates different biogeochemical processes, including aerobic degradation, denitrification, manganese reduction, iron reduction, sulfate reduction and methanogenesis. The model was able to describe and quantify these complex biogeochemical processes. The proposed model offers a rational framework for simulating coupled reactive transport processes occurring beneath a landfill site.