In this paper, groundwater flow models were created to assess the impact of hydrologic and operational parameters on the aquifer within the context of managed aquifer recharge project implementation. Flow/particle tracking models were used to track the movement of injected water during injection, storage and possible recovery. We used the software package COMSOL Multiphysics 4.3 and Visual MODFLOW to create the groundwater flow and transport models. This paper examines and compares the performance of both models. The simulation results show similar groundwater flow pattern in both models. Later on, COMSOL model was used to simulate different options of MAR project.