The Minesing Wetlands contain Canada’s only known population of Hine’s emerald dragonfly (HED), a species listed as endangered since 2011. The HED relies on groundwater discharge areas to complete its life cycle and therefore the population is potentially sensitive to changes in groundwater. The goals of this study were to, (1) characterize groundwater discharge to the eastern portion of the Minesing Wetlands, which corresponds to the HED habitat, (2) document any significant changes in groundwater chemistry since a 1998 study, and (3) establish a comprehensive baseline water quality data set to facilitate future comparisons. Consistent with HED habitats in the USA, the chemistry of Minesing Wetlands groundwater was dominated by calcium and bicarbonate. Low groundwater chloride and nitrate concentrations indicated minimal impact from activities such as road salt application and fertilizer use. Nitrate was generally only found at the wetland margin where groundwater springs emerged from the base of the uplands. The dominant form of inorganic nitrogen in wetland groundwater was ammonium (max = 1.5 mg N/L), and soluble reactive phosphorus concentrations were also relatively high (8 to 122 µg/L). The most consistent change in wetland groundwater chemistry between the 1998 study and samples collected in 2015–2017 was that chloride concentrations in 10 of 23 wells increased over time, however the maximum mean well chloride (11.6 mg/L) remained well below the guideline for the protection of aquatic life (120 mg/L). To preserve HED habitat, potential impacts to groundwater need to be considered during land use planning for the recharge area.