This paper addresses the problem of 14C age dating of groundwaters in a confined regional aquifer affected by methanogenesis. Increasing CH4 concentrations along the groundwater flow system and 13C and 14C isotopic data for dissolved inorganic carbon, dissolved organic carbon, and CH4 clearly show the effect of methanogenesis on groundwater chemistry. Inverse reaction path modeling using NETPATH indicates the predominant geochemical reactions controlling the chemical evolution of groundwater in the aquifer are incongruent dissolution of dolomite, ion exchange, methanogenesis, and oxidation of sedimentary organic matter. Modeling of groundwater 14C ages using NETPATH indicates that a significant part of groundwater in the Alliston aquifer is less than 13,000 years old; however, older groundwater in the range of 15,000–23,000 years is also present in the aquifer. This paper demonstrates that 14C ages calculated using NETPATH, incorporating the effects of methanogenesis on the carbon pools, provide reasonable groundwater ages that were not possible by other isotopic methods.