The Gabes region in southeastern Tunisia faces significant water stress due to limited water resources, with groundwater being the primary source for various human activities. The ongoing and future effects of global warming and climate change, characterized by rising temperatures and fluctuations in rainfall patterns, are set to exacerbate water scarcity and degrade the quality of this region's water resources. This study aimed to assess the impact of global warming and climate change on natural groundwater recharge in an unconfined aquifer system within the Gabes region utilizing the Markov chains methodology. To do so, future climatic parameters specific to the study area were projected by downscaling a general circulation model (GCM). Over the temporal period from 2020 to 2100, various climate change scenarios, including A1, A2, and B2, were employed to estimate the evolution of groundwater levels throughout the region. Upon analyzing historical data and employing the Markov chain method to forecast future scenarios, the downscaling modeling approach proved to be effective in predicting climate parameters such as average temperature, precipitation, and wind speed for the designated time frame. The results were visually represented as piezometric maps representing the different scenarios. It is important to note that there is predicted to be a general decline in precipitation, with an anticipated average decrease of 40 mm/year by the 2100s, particularly when considering potential increases in water abstraction rates. Consequently, groundwater recharge is expected to decrease, leading to a noticeable drawdown in groundwater levels across all three scenarios. This study sheds light on the critical implications of climate change for the Gabes region, highlighting the urgent need for sustainable water resource management and conservation measures to mitigate the adverse effects of decreasing groundwater availability.