The city of Cartagena and its immediate surroundings have experienced significant topographical changes throughout its history. Originally built on five hills which border south and west with the Mediterranean Sea, the city has expanded to the north over the last five decades, occupying a lacustrine system which has now dried up due to the diversion of riverbeds which, from time to time, used to flood the place. These changes have been documented and studied from the lithology present in over 400 geotechnical drillings carried out in the urban renewal of the city for the last two decades. In addition, another 20 new continuous drillings have been conducted within the Project “Surveying and planning a privileged Mediterranean city, Arqueotopos I and II” which is still ongoing. The information obtained is completed with the study of all existing historical maps on it. Digital Terrain Models (DTMs) have been generated with this drilling data, then several lithological layers have been selected for its interest: anthropic fill, mud and underlying bedrock. The thickness of each of the layers has been studied in different areas and viewed through various longitudinal profiles that have been plotted. Finally, a three-dimensional (3D) virtual reconstruction has been undertaken to see graphically the documented changes that have occurred in each of these layers, to serve both research and divulgation knowledge.