Estimating groundwater recharge in response to increased atmospheric CO2 concentration and climate change is critical for future management of agricultural water resources in arid or semi-arid regions. Based on climate projections from the Intergovernmental Panel on Climate Change, this study quantified groundwater recharge under irrigated agriculture in response to variations of atmospheric CO2 concentrations (550 and 970 ppm) and average daily temperature (+1.1 and +6.4 ◦C compared to current conditions). HYDRUS 1D, a model used to simulate water movement in unsaturated, partially saturated, or fully saturated porous media, was used to simulate the impact of climate change on vadose zone hydrologic processes and groundwater recharge for three typical crop sites (alfalfa, almonds and tomatoes) in the San Joaquin watershed in California. Plant growth with the consideration of elevated atmospheric CO2 concentration was simulated using the heat unit theory. A modified version of the Penman–Monteith equation was used to account for the effects of elevated atmospheric CO2 concentration. Irrigation amount and timing was based on crop potential evapotranspiration. The results of this study suggest that increases in atmospheric CO2 and average daily temperature may have significant effects on groundwater recharge. Increasing temperature caused a temporal shift in plant growth patterns and redistributed evapotranspiration and irrigation water use earlier in the growing season resulting in a decrease in groundwater recharge under alfalfa and almonds and an increase under tomatoes. Elevating atmospheric CO2 concentrations generally decreased groundwater recharge for all crops due to decreased evapotranspiration resulting in decreased irrigation water use. Increasing average daily temperature by 1.1 and 6.4 ◦C and atmospheric CO2 concentration to 550 and 970 ppm led to a decrease in cumulative groundwater recharge for most scenarios. Overall, the results indicate that groundwater recharge may be very sensitive to potential future climate changes.