Groundwater is an important factor in sustaining water supply in semi-arid coastal basins, where surface water resources are limited and climatic variability greatly affects availability. Rainfall events translated to groundwater recharge are of paramount importance for planning as well as for sustainable resource management in the Mediterranean catchment. The interaction between rainfall and groundwater level is particularly complex within areas of geological heterogeneity and seasonal climatic regimes. As valuable as this relationship is, it continues to be poorly understood in the most vulnerable areas, including western Syria. This research examines the dynamic interaction between rainfall and groundwater levels in the Al-Hsain Basin, a semi-arid coastal area in western Syria. A transient groundwater flow model was built with MODFLOW and calibrated against 4 y (2020–2024) of monthly data from 35 observation wells and local precipitation measurements. The model effectively replicated seasonal groundwater variations controlled largely by rain, and spatial variations related to geological heterogeneity. A (0–1) month time lag between rainfall maxima and groundwater response suggests delayed infiltration in the unsaturated zone. Model performance was tested with statistical and hydrograph analyses, illustrating excellent agreement against over 95 % of observed data. The results confirmed the model as it gave a hydraulic head distribution very similar to the monitoring wells data (variations of less than 0.10–0.25 m). Spatial maps and water balance overviews under wet and dry conditions proved the model's robustness under hydrological conditions. Despite some data limitations, this study offers helpful data on groundwater recharge processes and practical recommendations for improving water resource management in similar Mediterranean coastal settings.