Hemerocallis esculenta suffered frost damage during a night of remarkably low temperatures at Sarobetsu Mire, northern Japan, on 5 June 2002. A numerical model simulation was conducted to evaluate how groundwater conditions affected the nocturnal air temperature at the mire. The numerical model developed in this study reproduced the nighttime cooling process of the air temperature profile at high resolution. The lowest water table level occurred at the site several days before 5 June. The numerical simulation suggested that if the lowest water table occurred on 5 June, under the same water table level, the minimum air temperature 0.2 m above the peat surface would have been 1.2°C higher because of the difference of volumetric water content. The rate of air temperature decrease at 0.2 m height to the water table decrease would be 0.7°C cm⁻¹. Therefore, the minimum air temperature near the peat surface of the mire is affected by both decreases in the water table level and the lowest depth prior to the observation day. Ensuring a high water table level could mitigate extreme low temperatures and frost damage at the mire.