Density-driven advection of gas phase due to vaporization of chlorinated volatile organic compounds (VOCs) has a significant effect on fate and transport of contaminants. In this study, we investigated the effects of density-driven advection, infiltration, and permeability on contaminant plume evolution and natural attenuation of VOCs in the subsurface system. To analyze these effects, multiphase flow and contaminant transport processes were simulated using a three-dimensional Galerkin-finite-element-based model. Trichloroethylene (TCE) is selected as a target contaminant. Density-driven advection of gas phase elevated the potential of groundwater pollution in the saturated zone by accelerating downward migration of vaporized contaminant in the unsaturated zone. The advection contributed to increased removal rates of non-aqueous phase liquid (NAPL) TCE source and reduced dissolved TCE plume development in the downstream area. Infiltration reduced the velocity of the density-driven advection and its influence zone, but raised TCE transfer from the unsaturated to the saturated zone. The variation in soil permeability showed greater impact on contaminant migration within water phase in the saturated zone than within gas phase in the unsaturated zone. Temporal variations of TCE mass within two-dimensional (2D) and three-dimensional (3D) domains under several modeling conditions were compared. These results are important in evaluation of natural attenuation processes, and should be considered to effectively design monitored natural attenuation as a remedial option.