In the last decade, production of shale gas has tremendously increased, and the need for local pre-exploitation baseline data on dissolved natural gas in aquifers has been stressed. This study investigated the origin of hydrocarbons naturally present in shallow aquifers of the Saint-Édouard area (Québec, eastern Canada), where the underlying Utica Shale is known to contain important gas resources that have not yet been exploited. Groundwater and shallow bedrock gas samples were collected and analyzed for isotopic composition of alkanes (δ13C and δ2HC1–C3), dissolved inorganic carbon (δ13CDIC), and radiocarbon in methane and DIC (14CDIC, 14CCH4). This multi-isotope approach proved enlightening, and results revealed that (1) most of the methane in the region is of microbial origin; (2) partial contribution of thermogenic gas occurs in 15% of the wells; (3) processes such as late-stage methanogenesis and methane oxidation are responsible for ambiguous methane isotopic compositions; and (4) both microbial and thermogenic gas originate from the shallow bedrock aquifer, with the exception of one sample likely coming from deeper units. The thick succession of shales overlying the Utica Shale thus appears to act as an effective migration barrier for the shallow aquifers. However, evidence of upward migration of old brines near major fault zones indicates that these may serve as a preferential migration pathway over a certain depth but most likely no more than approximately 200–500 m (∼650–1640 ft). The geochemical framework presented here will hopefully be useful in other research projects, especially when conventional indicators of natural gas origin provide ambiguous results.