Monitoring wells are often installed in aquitards to verify effectiveness for preventing migration of surface contaminants to underlying aquifers. However, water sampling of aquitard wells presents a challenge due to the slow recovery times for water recharging the wells, which can take as long as weeks, months or years to recharge depending on the sample volume needed. In this study, downhole profiling and sampling of aquitard wells was used to assess geochemical changes that occur in aquitard wells during water level recovery. Wells were sampled on three occasions spanning 11 years, 1 year and 1 week after they were purged and casing water showed substantial water chemistry variations. Temperature decreased with depth, whereas pH and specific conductance increased with depth in the water column after 11 years of water level recovery. Less stable parameters such as dissolved O₂ (DO) and Eh showed strong zonation in the well column, with DO stratification occurring as the groundwater slowly entered the well. Oxidation of reduced till groundwater along with degassing of CO₂ from till pore water affects mineral solubility and dissolved solid concentrations. Recommendations for sampling slowly recovering aquitard wells include identifying the zone of DO and Eh stratification in the well column and collecting water samples from below the boundary to better measure unstable geochemical parameters.