Environmental concerns regarding the potential for drinking water contamination in shallow aquifers have accompanied unconventional energy development in the northern Appalachian Basin. These activities have also raised several critical questions about the hydrogeological parameters that control the naturally occurring presence and migration of hydrocarbon gases in shallow aquifers within petroliferous basins. To interrogate these factors, we analyzed the noble gas, dissolved ion, and hydrocarbon gas (molecular and isotopic composition) geochemistry of 98 groundwater samples from south-central New York. All samples were collected ≫1km from unconventional drilling activities and sample locations were intentionally targeted based on their proximity to various types of documented fault systems. In agreement with studies from other petroliferous basins, our results show significant correlations between elevated levels of radiogenic [ He], thermogenic [CH ], and dissolved ions (e.g., Cl, Br, Sr, Ba). In combination, our data suggest that faults have facilitated the transport of exogenous hydrocarbon-rich brines from Devonian source rocks into overlying Upper Devonian aquifer lithologies over geologic time. These data conflict with previous reports, which conclude that hydrodynamic focusing regulates the occurrence of methane and salt in shallow aquifers and leads to elevated levels of these species in restricted flow zones within valley bottoms. Instead, our data suggest that faults in Paleozoic rocks play a fundamental role in gas and brine transport from depth, regulate the distribution of their occurrence in shallow aquifers, and influence the geochemistry of shallow groundwater in this petroliferous basin.