A GIS project was created in order to manipulate and present geophysical and topographical data from the archaeological site of Itanos, Crete, Greece. This GIS project can handle different types of geophysical images such as maps, depth or time slices, depth sections and three-dimensional images. Thematic information such as type of measurement, station spacing, size of the profile or grid can also be retrieved for each geophysical image. Another feature of the project is the superposition of selected geophysical images and other types of datasets like aerial photographs, as well as archaeological, geological and elevation maps. The combination of maps led to an easier way of presentation and a more valid interpretation of geophysical data. The outline of the ancient port of Itanos was revealed by combining seismic, soil resistance, magnetic gradient and soil conductivity data with a 3D elevation model of the site.