Groundwater depletion coupled with climate change, increasing temperature, and decreasing precipitation, has led to groundwater quality deterioration and diminishing groundwater quantity, subsequently affecting agricultural productivity in arid environments. The groundwater of the Al-Baha region, Saudi Arabia is located in unconfined shallow aquifers and responds quickly to climate change. The Al-Baha region is facing an increase in temperature and a substantial decrease in precipitation. Over the 24-year period from 1995 to 2019, average temperatures increased by 1.1 °C–1.6 °C, while rainfall decreased by 24–41%. Consequently, this study aimed at investigating the influence of climate change on soil salinity and pomegranate productivity. To achieve this goal, a hundred and fifteen samples of soil and groundwater were collected from different locations in the Al-Baha region. Furthermore, the SALTMED model was calibrated using the salinities of 50 groundwater samples, which are used as irrigation water, and climatic data from the year 2020. The model was then validated using 65 irrigation water salinities and climatic data from the year 2020. Pomegranate fruit yield was used as the main variable for calibration and validation. After successful calibration and validation, the SALTMED model was run using ‘what if’ scenarios for the years 2044, 2068, and 2092. It is assumed that the temperature will increase, while the annual rainfall will decrease in upcoming decades. Consequently, the groundwater salinities will reach 1.44, 2.59, and 4.67 dS m−1 for the years 2044, 2068, and 2092, respectively. The results revealed that the soil salinities will increase by 113%, 300%, and 675%, respectively, compared with the average soil salinity of the year 2020 (2.22 dS m−1). Furthermore, the pomegranate tree productivity in the Al-Baha region will decrease significantly (24.0%, 36.6%, and 41.6%) in the predicted three years due to deterioration of groundwater quality and increasing temperatures. Interventions by the regional authorities to minimize the impact of climate change on crop and fruit productivity and groundwater deterioration in the Al-Baha region should be planned and carried out as soon as possible. The method used in this investigation can be utilized in similar ecosystems worldwide.