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Assessing the relationship between climate forcings and groundwater recharge (GR) rates in semi-arid regions is critical for water resources management. This study presents the impact of climate forecasts on GR within a probabilistic framework in a site-specific study in the Nebraska Sand Hills (NSH), the largest stabilized sand dune region in the USA containing the greatest recharge rates within the High Plains Aquifer. A total of 19 downscaled climate projections were used to evaluate the impact of precipitation and reference evapotranspiration on GR rates simulated by using HYDRUS 1-D. The analysis of the decadal aridity index (AI) indicates that climate class will likely remain similar to the historic average in the RCP2.6, 4.5, and 6.0 emission scenarios but AI will likely decrease significantly under the worst-case emission scenario (RCP8.5). However, GR rates will likely decrease in all of the four emission scenarios. The results show that GR generally decreases by similar to 25% under the business-as-usual scenario and by nearly 50% in the worst-case scenario. Moreover, the most likely GR values are presented with respect to probabilities in AI and the relationship between annual-average precipitation and GR rate were developed in both historic and projected scenarios. Finally, to present results at sub-annual time resolution, three representative climate projections (dry, mean and wet scenarios) were selected from the statistical distribution of cumulative GR. In the dry scenario, the excessive evapotranspiration demand in the spring and precipitation deficit in the summer can cause the occurrence of wilting points and plant withering due to excessive root-water-stress. This may pose significant threats to the survival of the native grassland ecology in the NSH and potentially lead to desertification processes if climate change is not properly addressed.