Ground-penetrating radar (GPR) techniques have been progressively developed to investigate several types of subsurface sedimentary features particularly in the upper zone of carbonate rocks. Most of common subsurface sedimentary heterogeneities such as karst in the western carbonate plateau of Assiut were formed by natural processes. Detection of the karst is very important to face up the expected socio-economical pressure, resulting from the dense population around the Nile Valley and important for the cement industry. These heterogeneities represent anomalies or departures from the surrounding or “background” geologic conditions which make them easier to detect by GPR. All the GPR profiles are made using an antenna 200 MHz. The 400 MHz antenna is used only to get more details on one of the detected abnormal zones. A series of the 3D model cross-section with variable depths in addition to 3D modules for the karst is constructed to ascertain the existence and the characteristics of these features. The careful analysis of the upper part of constructed GPR cross-section in the area is implemented by a digital three-dimensional model. It is believed that the examined area which having low-contrast variable-depth heterogeneities (karst features) may give a satisfactory outcome only by 3D simulation. This study indicates significant potential for the presence of karst in different locations and depths.