Airborne magnetic data set of  Qena as well as the eastern margin of the Western Desert has been processed to estimate the depth of the basement, and accordingly the thickness of the sedimentary cover that could give some information about the groundwater potentiality in the area under consideration. Reduced to Pole Magnetic Map (RTP), Butterworth Low Pass Filter, and Butterworth High Pass Filter have been used to represent the aeromagnetic data. Depths of the basement were estimated by using both the source parameter imaging technique (SPI) and radial average power spectrum technique (RAPS). According to the results of the (RAPS) technique, the estimated average depths of deep and shallow magnetic sources are 2.331 km and 0.50 km respectively. On the other side, the (SPI) technique emphasized that the depth to reach crystalline basement rocks varies between -551 m to -2817 m. The southern and western portions of the target area are particularly distinguished by thick sedimentary cover. These portions may be areas with high potentialty of groundwater.