The unmanaged groundwater extraction and inadequate aquifer recharge is the major cause of groundwater depletion in different parts of the world. In this study, the groundwater flow system of Mahvelat-Feizabad aquifer (NE of Iran) has been numerically simulated using MODFLOW code in the GMS interface. The model, primarily, calibrated for steady state condition for the mean hydraulic values of one-year period (Sep. 2012 to Sep. 2013) which has steady condition with low stresses on aquifer. Then the model is run/calibrated for transient condition for one year period (Sep. 2012 to Sep. 2013). After determining the hydraulic properties of the aquifer and confirming their validity, different scenarios were applied to the model. Results show that, by continuing the current aquifer conditions, there will be a constant decrease in water level with the approximate rate of 0.8 m/year. Changing the exploitation of water from critical zone and overexploitation from saline water zone will affect the critical zone by causing a sharp decline in water level as well as its affection in water quality parameters that directly affect the agriculture of this area. Results show that proper management of aquifer can affect the groundwater flow direction and extent of saline water zone. In addition, artificial recharge which contain direct and indirect technique such as percolation tank and injection well and spreading channel are all the preventative measures to overcome the expansion of saline water zone.