A multi‐phase, multi‐component model which describes contaminant transport in the unsaturated zone is developed in this work. The model incorporates the heterogeneity of pore fluid distribution and inducing gas‐phase advective transport. The numerical approximation scheme consists of finite difference method and the method of characteristics. For solving the system of equations, the method of over‐relaxation is employed. This model has been verified by a one‐dimensional analytical solution. The application of the model to the soil vapor extraction (SVE) system further demonstrates the suitability of the model. From analyzing the results from the application, we found that gas‐phase transport of volatile contaminants nearly above the water table is relatively ineffective (due to low volumetric content of pore air and correspondingly low gas‐phase permeability). In addition to the assessment of the effectiveness of SVE systems, aqueous‐gas interphase mass transfer is observed dominating the contaminant transport during the process of sensitivity analysis. Therefore, Henry's law constant is strongly suggested to be included in the definition of mobility of volatile organic contaminants in the unsaturated zone.