Cold groundwater discharge to streams and rivers can provide critical thermal refuge for threatened salmonids and other aquatic species during warm summer periods. Climate change may influence groundwater temperature and flow rates, which may in turn impact riverine ecosystems. This study evaluates the potential impact of climate change on the timing, magnitude, and temperature of groundwater discharge from small, unconfined aquifers that undergo seasonal freezing and thawing. Seven downscaled climate scenarios for 2046–2065 were utilized to drive surficial water and energy balance models (HELP3 and ForHyM2) to obtain future projections for daily ground surface temperature and groundwater recharge. These future surface conditions were then applied as boundary conditions to drive subsurface simulations of variably saturated groundwater flow and energy transport. The subsurface simulations were performed with the U.S. Geological Survey finite element model SUTRA that was recently modified to include the dynamic freeze-thaw process. The SUTRA simulations indicate a potential rise in the magnitude (up to 34%) and temperature (up to 3.6°C) of groundwater discharge to the adjacent river during the summer months due to projected increases in air temperature and precipitation. The thermal response of groundwater to climate change is shown to be strongly dependent on the aquifer dimensions. Thus, the simulations demonstrate that the thermal sensitivity of aquifers and baseflow-dominated streams to decadal climate change may be more complex than previously thought. Furthermore, the results indicate that the probability of exceeding critical temperature thresholds within groundwater-sourced thermal refugia may significantly increase under the most extreme climate scenarios.