The three-dimensional groundwater flow model MODFLOW was applied to simulate water level change in the complex multi-aquifer systems (the Upper and Middle Aquifers) of the Azraq basin. The model was calibrated by matching observed and simulated drawdown for steady and transient states over the period 1970–1992. Drawdown data for the period 1993–1997 were used to test the model's ability to predict the response of the aquifers. The model performed well in representing the water level contours of the Upper and Middle Aquifers for steady state calibration. Agreement between the observed and simulated drawdowns was obtained for transient state calibration. To predict the aquifer system responses for the period of 1997–2025, four different pumping schemes (scenarios) have been investigated. The first scenario (present pumping rate) reveals that there will be approximately a 25 m drop in the water level at the well-field area in 2025. However, the worst scenario (pumping rate at 1.5 times the present rate) reveals an approximate 39 m drop in the water level at the well-field area in 2025. The safe yield for the Upper Aquifer System was found to be about 25 million cubic meters (MCM) yearly.