The need to consider aqueous and sorption reaction kinetics and microbiological processes arises in many subsurface problems. By adding these processes to the TOUGH family code, more complex problems can be addressed that involve multiphase fluid and heat flow, and geochemical interaction. This paper presents a formulation for incorporating kinetic rates among primary species into mass-balance equations. The space discretization used is based on a flexible integral finite difference approach that uses irregular gridding to model biogeologic structures. A general multiregion model for hydrological transport interacted with microbiological and geochemical processes is proposed. A one-dimensional reactive transport problem with kinetic biodegradation and sorption was used to test the enhanced simulator, which involves the processes that occur when a pulse of water containing nitrylotriacetate (NTA) and cobalt is injected into a column. The current simulation results agree very well with those obtained with other simulators. The applicability of this general multiregion model was validated by results from a published column experiment of denitrification and sulfate reduction. The matches with measured nitrate and sulfate concentrations were adjusted with the interfacial area between mobile and immobile regions. Results suggest that TOUGHREACT not only is useful interpretative tool for biogeochemical experiments but also can produce insight into processes and parameters of microscopic diffusion and their interplay with biogeochemical reactions.