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Shallow groundwater in the Prairie Pothole Region (PPR) is recharged predominantly by snowmelt in the spring and may supply water for evapotranspiration through the summer/fall. This two-way exchange is underrepresented in land-surface models. Furthermore, the impacts of climate change on the groundwater recharge are uncertain. In this paper, we use a coupled land and groundwater model to investigate the hydrologic cycle of shallow groundwater in the PPR and study its response to climate change at the end of the 21st century. The results show that the model reasonably simulates the water table depth (WTD) and the timing of recharge processes, but underestimates the seasonal variation of WTD, due to mismatches of the soil types between observations and the model. The most significant change under future climate occurs in the winter, when warmer temperature changes the rain/snow partitioning, delay the time for snow accumulation/soil freezing while bring forward early melting/thawing. Such changes lead to an earlier start to a longer recharge season, but with lower recharge rates. Different signals are shown in the eastern and western PPR in the future summer, with reduced precipitation and drier soils in the east but little change in the west. The annual recharge increased by 25% and 50% in the eastern and western PPR, respectively. Additionally, we found the mean and seasonal variation of the simulated WTD are sensitive to soil properties and fine-scale soil information is needed to improve groundwater simulation on regional scale.