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Fluid flux through aquitards controls the rate of recharge, discharge, cross-formational fluid flow and contaminant transport in subsurface systems. In this paper, concentrations of He-4 are used to investigate the spatial distribution of vertical fluid flux through the regionally extensive Great Artesian Basin aquitard system in northern South Australia. Two vertical profiles of He-4 concentration in aquitard pore water, augmented with regional sampling of aquifers above and below the aquitard were used to estimate fluid flux at multiple locations over a large spatial area. He-4 concentrations in the shallow aquifer above the Great Artesian Basin range from atmospheric equilibrium to 1000 times enriched over atmosphere. Fluid flux through the aquitard was estimated by fitting observed helium concentrations at each sampling site with a 1-D model of helium transport through the aquitard. Estimated fluid fluxes through the aquitard vary over three orders of magnitude across the study area. In areas of competent aquitard, fluid fluxes are less than 0.003 mm/yr, and mass transport of helium is dominated by molecular diffusion. Preferential discharge zones are clearly identifiable with fluid fluxes up to 3 mm/yr. Our results show that fluid flux through a regionally extensive aquitard can be highly variable at large spatial scales, and that He-4 concentrations in aquifers bounding the aquitard system provide a convenient and sensitive method for investigating aquitard flux at the regional scale. (C) 2012 Elsevier B.V. All rights reserved.