Groundwater is one of the major parameters in maintaining ecology in many regions. As climate is one of the main factors which affects groundwater resources, the main objective of the present study is to assess the impact of rainfall changes on the groundwater system by projecting the future changes in the 21st century (2021-2050 and 2071-2100). For this reason, the RegCM3 climate model precipitation data, which showed a reduction in rainfall, was entered in the steady-state groundwater flow model MODFLOW for the case study of a coastal aquifer in the eastern part of the Thermaikos Gulf (North Greece). The uprising urbanization in combination with the intensive cultivation have led to the overexploitation of the coastal aquifer and seawater intrusion. The groundwater flow simulation by using the MODFLOW code indicates a negative water budget and estimates the quantities of the seawater intrusion. According to the RegCM3 climate model, the precipitation reduction is estimated to be 4% during the period of 2021-2050, while the precipitation decrease is expected to be 22% during the period of 2071-2100. Furthermore, the natural recharge of the coastal aquifer is expected to be influenced by the precipitation reduction. Finally, the seawater intrusion amounts are expected to increase during these future periods and more specifically during the second period of 2071-2100.