Water shortage is the main problem facing any development in Egypt especially in the desert lands. River Nile is considered the main source of water in Egypt but its water covers only the area of flood plain where its tributaries do not reach to the desert. The desert fringes, west of El-Minia governorate, Egypt, are areas of natural expansion for agricultural, industrial, and civil activities. This implies an increasing demand for groundwater. A numerical groundwater model is one of the main tools used for assessment of the resource potential and prediction of future impact under different circumstances and stresses. In this paper, a transient groundwater flow model in the desert district west of El-Minia, Egypt, was developed. The conceptual model was built by analyzing the hydrogeological data and previous work. Steady state model of year 1990 was used to investigate and calibrate the parameters such as hydraulic conductivities, recharge and conductance of the surface water streams. The storage coefficients are calibrated by the transient model based on the available data observed from 1990 to 2013, which provides insights to understand the behavior of groundwater system in Quaternary Aquifer and to predict spatial-temporal distributions of groundwater levels and groundwater flow in responding to extraction of water. The calibrated transient model will be used to predict the impacts of desert development schemes and water resources management schemes on groundwater in the study area.