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In this work, a 3D groundwater flow model integrating all important geological features of the hydrogeological system is developed to investigate hydrological processes in the Wadi Kafrein area of Jordan. A large amount of available geological and hydrological data is integrated to construct a 3D groundwater flow model for the Wadi Kafrein area. Using the newly developed mapping approach, the translation of the highly detailed geological formations to an unstructured finite element grids, can be accomplished with high precision. The existing data set for model calibration is scarce, which is a typical situation for many hydrogeological case studies. At first, the steady state calibration of the groundwater model is carried out based on the observation wells. Then, the time and space-dependent recharge from precipitation are applied at the top surface of the finite element model. The transient simulation is conducted during the period of 1996-2008 considering the abstraction rates of the production wells and discharge of the springs. The calculated water levels are close to the observed values. The difference is partly caused by return flows from irrigation and the groundwater inflow from the adjacent aquifers which are not taken into consideration so far. Since the Wadi Kafrein area is an important agricultural area in the semiarid region of the Lower Jordan Valley, the model developed in this study can be regarded as a useful tool for analyzing the hydrological processes and improving groundwater management practices elsewhere affected by similar geological and hydrogeological conditions.