Subsurface contamination by organic chemicals is a pervasive environmental problem, susceptible to remediation by natural or enhanced attenuation approaches or more highly engineered methods such as pump-and-treat, amongst others. Such remediation approaches, along with risk assessment or the pressing need to address complex scientific questions, have driven the development of integrated modelling tools that incorporate physical, biological and geochemical processes. We provide a comprehensive modelling framework, including geochemical reactions and interphase mass transfer processes such as sorption/desorption, non-aqueous phase liquid dissolution and mineral precipitatation/dissolution, all of which can be in equilibrium or kinetically controlled. This framework is used to simulate microbially mediated transformation/degradation processes and the attendant microbial population growth and decay. Solution algorithms, particularly the split-operator (SO) approach, are described, along with a brief résumé of numerical solution methods. Some of the available numerical models are described, mainly those constructed using available flow, transport and geochemical reaction packages. The general modelling framework is illustrated by pertinent examples, showing the degradation of dissolved organics by microbial activity limited by the availability of nutrients or electron acceptors (i.e., changing redox states), as well as concomitant secondary reactions. Two field-scale modelling examples are discussed, the Vejen landfill (Denmark) and an example where metal contamination is remediated by redox changes wrought by injection of a dissolved organic compound. A summary is provided of current and likely future challenges to modelling of oxidisable organics in the subsurface.