A 3D mathematical model that describes transport of volatile organic compounds in a coupled vadose-saturated zone system is proposed. The subsurface processes incorporated in the model include advection, dispersion, interphase mass transfer, and diffusive mass exchange between two horizontal porous media formations, as well as the time-dependent mass loading from a source zone. The analytical solutions are derived subject to the specific initial and boundary conditions. The solutions are evaluated by numerical Laplace inverse transform. The model solutions can be used to study the fate and transport in subsurface formations composed of a vadose zone and a water table aquifer, where the volatile organic compound is released from entrapped nonaqueous phase liquid in the vadose zone, or the dissolved volatile organic compound transports with groundwater accompanied by diffusive mass transfer into the overlying soil formations. Mass transfer between two layers is demonstrated to have back-diffusion characteristics, which results in secondary contamination and retains low levels of contaminant concentrations over a prolonged period of time. The model solutions are specifically useful in assessing the vapor intrusion process in a contaminated site where a vadose zone is underlain by a water table aquifer contaminated with volatile organic compounds.