This study presents the development of a finite difference groundwater flow model for the Sandy Complex aquifer system located in the Ergene River Basin in Thrace Peninsula of Turkey. Geological data is used in collaboration with the hydrogeological data to define the aquifer and its geometry. Distributions of hydraulic parameters and recharge are estimated by kriging methods and hydrologic simulations, respectively. The finite difference model with 5903 cells was used to represent the steady and unsteady flow in the aquifer. The simulations were carried out by using the MODFLOW code. The model was calibrated in two steps: a steady state calibration by using the observed groundwater levels of January 1970, followed by a transient calibration by using the observed groundwater levels for the period of January 1970 and December 2000. The results show that the model is capable of simulating the changes in water levels and groundwater budget components.