This study investigated the impact of climate change on water resources and the propagation of climate model variations in the Almyros basin, Greece, with a particular focus on the intensively utilized groundwater reserves essential for irrigation. Facing significant degradation in both their quantity and quality, understanding the future trajectory of groundwater resources is imperative. Climate change effects are evaluated through the employment of bias-corrected Med-CORDEX climate model projections, specifically considering the RCP8.5 emission scenario. Utilizing an Integrated Modelling System (IMS) comprising surface hydrology (UTHBAL) and groundwater hydrology (MODFLOW) modules, the future status of coastal water resources was simulated. The methodology involved a multi-step process: First, we acquired climate model data for various future climate model simulations. Subsequently, these data were used as an input for an Integrated Modelling System (IMS) simulating variables like recharge rates, evapotranspiration, groundwater levels, and others. The findings provide crucial insights for sustainable water resource management in the Almyros basin amidst changing climatic conditions. Through this approach, this study aimed to elucidate the propagation of climate model variability in the hydrological variables and processes, and it highlights the necessity of integrating advanced climate model projections with comprehensive hydrological modelling to project and estimate the variability of climate change impacts on coastal groundwater systems.