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Development of unconventional energy resources such as shale gas and coalbed methane has generated some public concern with regard to the protection of groundwater and surface water resources from leakage of stray gas from the deep subsurface. In terms of environmental impact to and risk assessment of shallow groundwater resources, the ultimate challenge is to distinguish (a) natural in situ production of biogenic methane, (b) biogenic or thermogenic methane migration into shallow aquifers due to natural causes, and (c) thermogenic methane migration from deep sources due to human activities associated with the exploitation of conventional or unconventional oil and gas resources. This study combines aqueous and gas (dissolved and free) geochemical and isotope data from 372 groundwater samples obtained from 186 monitoring wells of the provincial Groundwater Observation Well Network (GOWN) in Alberta (Canada), a province with a long record of conventional and unconventional hydrocarbon exploration. We investigated whether methane occurring in shallow groundwater formed in situ, or whether it migrated into the shallow aquifers from elsewhere in the stratigraphic column. It was found that methane is ubiquitous in groundwater in Alberta and is predominantly of biogenic origin. The highest concentrations of biogenic methane (> 0.01 mM or > 0.2 mgL−1), characterized by δ13CCH4 values 3, and Na-HCO3-Cl type groundwaters with negligible concentrations of nitrate and sulfate suggesting that methane was formed in situ under methanogenic conditions for 39.1 % of the samples. In only a few cases (3.7 %) was methane of biogenic origin found in more oxidizing shallow aquifer portions suggesting limited upward migration from deeper methanogenic aquifers. Of the samples, 14.1 % contained methane with δ13CCH4 values > −54 ‰, potentially suggesting a thermogenic origin, but aqueous and isotope geochemistry data revealed that the elevated δ13CCH4 values were caused by microbial oxidation of biogenic methane or post-sampling degradation of low CH4 content samples rather than migration of deep thermogenic gas. A significant number of samples (39.2 %) contained methane with predominantly biogenic C isotope ratios (δ13CCH4 δ13C) and thermogenic (presence of C3) characteristics, are most likely derived from shallow coal seams that are prevalent in the Cretaceous Horseshoe Canyon and neighboring formations in which some of the groundwater wells are completed. The remaining 3.7 % of samples were not assigned because of conflicting parameters in the data sets or between replicates samples. Hence, despite quite variable gas concentrations and a wide range of δ13CCH4 values in baseline groundwater samples, we found no conclusive evidence for deep thermogenic gas migration into shallow aquifers either naturally or via anthropogenically induced pathways in this baseline groundwater survey. This study shows that the combined interpretation of aqueous geochemistry data in concert with chemical and isotopic compositions of dissolved and/or free gas can yield unprecedented insights into formation and potential migration of methane in shallow groundwater. This enables the assessment of cross-formational methane migration and provides an understanding of alkane gas sources and pathways necessary for a stringent baseline definition in the context of current and future unconventional hydrocarbon exploration and exploitation.