Methane leakage due to compromised hydrocarbon well integrity can lead to impaired groundwater quality. Here we use a three‐dimensional, multiphase (vapor and aqueous), multicomponent (methane, water, salt), numerical model (TOUGH2 EOS7C) to investigate hydrogeological conditions that could result in groundwater contamination from natural gas wellbore leakage that migrates upward toward a freshwater aquifer. The conceptual model used for the simulations assumes methane leakage at 20–30 m below groundwater. We perform 180 simulations for a sensitivity analysis, examining (1) multiphase flow parameters related to storage, capillarity, and relative permeability, including porosity (ϕ), initial fluid‐phase saturation (SL), and van Genuchten n and α, (2) geostatistical variations in intrinsic permeability (ki), and (3) methane source‐zone pressure. Simulated mean ki values are 10−18 and 10−13 m2 with variances of 1 and 5 m4. Simulated source‐zone pressures range from just over ambient hydrostatic pressure at the depth of leakage (100 kPa) to the maximum pressure that steel casings are commonly rated to withstand (20,340 kPa). ki, initial SL, ϕ, and van Genuchten's n and α were the most important parameters in determining the volume of methane reaching groundwater during a given time period. Multiphase parameterization of formations underlying freshwater aquifers and overlying hydrocarbon production zones is fundamental to assessing aquifer vulnerability to methane leakage.