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In this paper, the physiography, geomorphological features, and sedimentary bedforms of the offshore Egadi Islands (Italy) have been illustrated and mapped through an integrated analysis of high-resolution bathymetric, seismo-acoustic, and sedimentological data. The study area is characterized by a wide, up to 25 km, continental shelf which is separated by a NNW-trending linear incision, the Marettimo Channel, along which several erosional and depositional features have been detected and mapped. Sedimentary prograding wedges were detected at water depths between 100–125 m along the shelf margin, which accumulated during the sea-level fall and lowstand stages of the last glacio-eustatic cycle (post- MIS 5.5). This study detected several slope breaks defining scarps across the continental shelf, which were interpreted as coastal cliffs that originated during the post-LGM eustatic sea-level rise. Several fields of different types of sedimentary bedforms, including 2-D and 3-D hydraulic dunes and sorted bedforms, were found across the continental shelf, providing evidence of a high hydrodynamic regime affecting the seafloor. Further on, this study recognized erosive and depositional features related to bottom currents (contourites) in the Marettimo Channel. These findings provide a better understanding of the morpho-sedimentary evolution of the Egadi Islands offshore in the latest Quaternary. Moreover, they offer essential scientific support for effectively managing the most valuable priority habitats for conservation, such as the <i>Posidonia oceanica</i> meadow and coralline algae bioconstructions (<i>Coralligenous</i> habitat).