The current strong motivation to explore those traces of the archaeological and prehistoric human heritage that presently lie submerged on the continental shelf requires large-scale and precise underwater mapping. One Mediterranean sector deserving particular attention is the Sicily Channel, which is critical for a better understanding of the Africa–Europe migratory routes and early civilization patterns due to its large expanses of shallow seabed that were partially or totally exposed at times of lower relative sea levels. We have focused our attention on the submerged continental margin of the Maltese archipelago. A detailed bathymetric map is here presented, and is discussed in terms of features interpretable as former subaerial landforms and inundated by sea-level rise following the Last Glacial Maximum lowstand at approximately –130 m. Our datasets combine multibeam surveys, Light Detection And Ranging (LiDAR)-derived digital terrain models (DTMs), Chirp sub-bottom profiler records and bottom samples acquired between 2009 and 2012. The main features identified are former river incisions, alluvial plains, karst landscapes (sinkholes, limestone plateaus), slide deposits and palaeoshorelines. This study provides a detailed topographical reconstruction of the palaeolandscape of this key region that is relevant to any future archaeological exploration of the Maltese offshore area.