A multiphase flow and transport numerical model is developed to study the effects of porous media heterogeneities on residual NAPL mass partitioning and transport of dissolved and/or volatilized NAPL mass in variably saturated media. The results indicate the significance of porous media heterogeneity in influencing the mass transfer processes and NAPL transport in the subsurface. Among the parameters investigated in this study, the heterogeneity of the permeability field has the most significant influence on the NAPL mass partitioning and transport. In general, the heterogeneity of the porous media properties enhances the NAPL mass plume spreading in both the water phase and the gas phase while the influence on the water phase is much more significant. Overall, the porous media property heterogeneities tend to increase the accumulation of NAPL mass in the water phase. The nonequilibrium mass transfer processes result in the expected trend of decreasing the NAPL mass dissipation rate and causing long-term groundwater contamination.