Baseline groundwater geochemical mapping of inorganic and isotopic parameters across 44,000 km2 of southwestern Ontario (Canada) has delineated a discreet zone of natural gas in the bedrock aquifer coincident with an 8,000-km2 exposure of Middle Devonian shale. This study describes the ambient geochemical conditions in these shales in the context of other strata, including Ordovician shales, and discusses shale-related natural and anthropogenic processes contributing to hydrogeochemical conditions in the aquifer. The three Devonian shales—the Kettle Point Formation (Antrim equivalent), Hamilton Group and Marcellus Formation—have higher DOC, DIC, HCO3, CO2(aq), pH and iodide, and much higher CH4(aq). The two Ordovician shales—the Queenston and Georgian-Bay/Blue Mountain Formations—are higher in Ca, Mg, SO4 and H2S. In the Devonian shale region, isotopic zones of Pleistocene-aged groundwater have halved in size since first identified in the 1980s; potentiometric data implicate regional groundwater extraction in the shrinkage. Isotopically younger waters invading the aquifer show rapid increases in CH4(aq), pH and iodide with depth and rapid decrease in oxidized carbon species including CO2, HCO3 and DIC, suggesting contemporary methanogenesis. Pumping in the Devonian shale contact aquifer may stimulate methanogenesis by lowering TDS, removing products and replacing reactants, including bicarbonate, derived from overlying glacial sedimentary aquifers.