© 2017 The Author(s) Gas flow through the vadose zone from sources at depth involves fractionation effects that can obscure the nature of transport and even the identity of the source. Transport processes are particularly complex in low permeability media but as shown in this study, can be elucidated by measuring the atmospheric noble gases. A series of laboratory column experiments was conducted to evaluate the movement of noble gas from the atmosphere into soil in the presence of a net efflux of CO2, a process that leads to fractionation of the noble gases from their atmospheric abundance ratios. The column packings were designed to simulate natural sedimentary deposition by interlayering low permeability ceramic plates and high permeability beach sand. Gas samples were collected at different depths at CO2 fluxes high enough to cause extreme fractionation of the noble gases (4He/36Ar > 20 times the air ratio). The experimental noble gas fractionation-depth profiles were in good agreement with those predicted by the dusty gas (DG) model, demonstrating the applicability of the DG model across a broad spectrum of environmental conditions. A governing equation based on the dusty gas model was developed to specifically describe noble gas fractionation at each depth that is controlled by the binary diffusion coefficient, Knudsen diffusion coefficient and the ratio of total advection flux to total flux. Finally, the governing equation was used to derive the noble gas fractionation pattern and illustrate how it is influenced by soil CO2 flux, sedimentary sequence, thickness of each sedimentary layer and each layer's physical parameters. Three potential applications of noble gas fractionation are provided: evaluating soil attributes in the path of gas flow from a source at depth to the atmosphere, testing leakage through low permeability barriers used to isolate buried waste, and tracking biological methanogenesis and methane oxidation associated with hydrocarbon degradation.