Multi-phase and multi-component numerical simulations have been carried out to investigate the migration behaviour of methane gas in shallow aquifers. The conceptual model includes methane leaking from a poorly sealed well into a heterogeneous aquifer with free-phase gas transport (methane and background gases) governed by capillary and buoyancy forces, dissolution of methane into flowing groundwater, and advective-diffusive transport of the dissolved phases. All simulations are carried out in three dimensions using the DuMux simulator assuming a continuum approach, applied to a 100 m long and 40 m thick sequence of fractured rock and Quaternary sediments in the Saint Lawrence Basin, southern Quebec, Canada. Simulation scenarios include continuous and intermittent leaks of multicomponent gas and varying groundwater flow velocities. A mass-balance analysis was also carried out to quantify the partitioning of leaked gas between the free-gas and dissolved phases, and to evaluate the proportion of methane retained in groundwater versus that emitted at the surface under different hydraulic and leakage conditions. The results focus on the effect of aquifer heterogeneity on plume behavior, showing that even thin low-permeability layers can lead to gas accumulation and enhanced mass transfer. Leakage of natural gas components (CH4 and C2H6) leads to decreased concentrations of background gases, especially N2, which can serve as a useful tracer for groundwater contamination. We highlight the implications of gas migration behavior on developing monitoring strategies based on the hydrogeological system and background flow field.