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In this work, a high precision groundwater flow model integrating all important geological features of the hydrogeological system is developed to investigate the hydrological processes in the Wadi Kafrein area. The object-oriented software OpenGeoSys (OGS) is applied and then updated in order to meet the challenges of complex geological features of the study area. The comparisons between the simulation results and the observation data show that the flow model is capable of reproducing historical groundwater level changes to a satisfactory degree. Since the Wadi Kafrein area is one of the arid and semiarid regions in the Lower Jordan Valley, the models developed in this study can be a useful tool for analyzing the hydrological processes and improving groundwater management practices elsewhere affected by similar geological and hydrogeological conditions.