Hydraulic fracturing is becoming an important technique worldwide to recover hydrocarbons from unconventional sources such as shale gas. In Quebec (Canada), the Utica Shale has been identified as having unconventional gas production potential. However, there has been a moratorium on shale gas exploration since 2010. The work reported here was aimed at defining baseline concentrations of methane in shallow aquifers of the St. Lawrence Lowlands and its sources using δ(13)C methane signatures. Since this study was performed prior to large-scale fracturing activities, it provides background data prior to the eventual exploitation of shale gas through hydraulic fracturing. Groundwater was sampled from private (n = 81), municipal (n = 34), and observation (n = 15) wells between August 2012 and May 2013. Methane was detected in 80% of the wells with an average concentration of 3.8 ± 8.8 mg/L, and a range of <0.0006 to 45.9 mg/L. Methane concentrations were linked to groundwater chemistry and distance to the major faults in the studied area. The methane δ(1)(3)C signature of 19 samples was > -50‰, indicating a potential thermogenic source. Localized areas of high methane concentrations from predominantly biogenic sources were found throughout the study area. In several samples, mixing, migration, and oxidation processes likely affected the chemical and isotopic composition of the gases, making it difficult to pinpoint their origin. Energy companies should respect a safe distance from major natural faults in the bedrock when planning the localization of hydraulic fracturation activities to minimize the risk of contaminating the surrounding groundwater since natural faults are likely to be a preferential migration pathway for methane.