Reactive transport modeling was employed to investigate the relative importance of fractionations associated with gas solubility, sorption and diffusive transport on dissolved methane, ethane and propane concentrations and the isotopic composition of carbon in methane (δ13C1) in groundwater. Temperature, pressure and salinity dependencies for the hydrocarbon gases were incorporated. Gas molecular ratios, C1/(C2 + C3), increased with diffusive transport, transitioning from thermogenic values to values typically indicative of biogenic gas sources, >1,000, at the leading edge of the diffusive front. Diffusive isotopic fractionation had a large effect on δ13C1 values, with fractionations ranging from −36‰ to −107‰, the difference being a function of the diffusive fractionation factor (αD0). Larger fractionations resulted from αD0 determined at relatively low pressures, 5–50 atm, and temperatures, 20°C–25°C. Less fractionation occurred with αD0 measured at higher pressures and temperature, 30–89 atm and 90°C. The extremely depleted δ13C1 values indicated from the modeling, less than −110‰, have not been observed in shallow groundwater, suggesting that diffusive fractionation of δ13C1 is offset by other processes such as microbial oxidation. 2k factorial analysis was used to assess the model sensitivity to specific parameters: estimations of hydrocarbon travel distance are most sensitive to porosity and tortuosity, while the molecular ratio was most sensitive to the free‐water diffusion coefficient, and the isotopic fractionation was most sensitive to αD0. The magnitude of diffusive fractionation on the molecular and isotopic composition of transported hydrocarbon gas may be similar to fractionations from microbial oxidation and mixing between different sources.