The bay of Malfatano Cape is the berthing home to one of the most important maritime structures from the Punic-Roman times in the Mediterranean. Two opposing monumental structures have been preserved between −7 and −2 m due to rising sea level. Recent studies have identified the paleo-sea level, relating the eustatic component to the glacio-hydroisostatic deformations. This paper, through stratigraphic, palaeontological, and geochronological data, aims to trace the bay of Capo Malfatano's evolution in relation to the sea level rise during the last 4 kys. Based on data derived from geophysical surveys, paleoshore lines have been redrawn and compared with data derived from coring in the inner part of the creek. Finally, we evaluated the relationship between changes in palaeogeography and human settlements from the Bronze Age. The breakwaters have been surveyed in detail using D-GPS techniques correlated to the geodesic 0 level. Through this data, the shape of the breakwaters has been reconsidered and, consequently, the palaeo sea level has been re-evaluated.