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PHT3D, a three-dimensional biogeochemical tool for natural and enhanced remediation of organic compounds in saturated porous media, is presented. The model is based on four modules: a three-dimensional transport model accounting for advective-dispersive transport and three modules accounting for (bio)chemical reactions. These comprise a NAPL (non aqueous phase liquids) dissolution module, a geochemical equilibrium package and a biodegradation module. The modules are coupled via an operator-splitting method. Model capabilities are demonstrated by way of an illustrative simulation for a dissolved hydrocarbon plume undergoing natural biogeochemical attenuation.