Standing column wells are a promising solution to reduce the environmental footprint of building energy consumption. Nevertheless, as in other open-loop wells, they can be affected by clogging processes if detrimental hydrogeological conditions are present locally. This problem is relatively rare and still difficult to anticipate, even though some specific factors have been reported, such as substratum mineralogy and groundwater quality. This study proposes the use of a column experiments and coupon cell to anticipate clogging at two different sites near Montréal, Canada. The experiments were performed for duration of 50 and 52 d using thermoregulated columns at four temperatures. The results identified a difference in the chemistry of each site without any significant clogging risk. Site A showed a decrease in carbonates, magnesium, and calcium ions, and scanning electron microscopy showed a minor tendency to form carbonate deposits. Sulfate and calcium dissolution of the bedrock material were observed at Site B. Scanning electron microscopy of the coupons revealed organic matter with high carbon and sulfate concentrations. The same type of deposits was observed at Site B after three years of operation. In conclusion, these tests helped identify various potential clogging phenomena and indicated that both sites are not susceptible to major clogging risks.