Augusta Bay is an embayment of the Hyblean sector in south-eastern Sicily (Southern Italy) that faces the Ionian Sea and includes the Rada di Augusta, a wide littoral sector sheltered by breakwaters, which hosts intense harbor activities. Rada di Augusta and the adjacent Priolo embayment were listed in the National Remediation Plan (NRP) by the Italian Ministry of Environment, as they have suffered major anthropic impacts over the last seventy years. Indeed, extensive petrochemical and industrial activities, military and commercial maritime traffic, as well as agriculture and fishery activities, have resulted in a highly complex combination of impacts on the marine environment and seafloor. In this paper, we investigate the extent of human-driven physical impacts on the continental shelf, offshore of Rada di Augusta, by means of Multibeam echosounder, Side-Scan Sonar and Chirp Sonar profilers, as well as direct seabed samplings. At least seven categories of anthropogenic footprints, i.e., anchor grooves and scars, excavations, trawl marks, targets, dumping trails, isolated dumping and dumping cumuli, mark the recent human activities at the seafloor. The practice of dredge spoil disposal, possibly protracted for decades during the last century, has altered the seafloor morphology of the central continental shelf, by forming an up-to-9 m-thick hummocky deposit, with acoustic features noticeably different from those of any other shelf lithosome originated by natural processes. All available data were reported in an original thematic map of the seafloor features, offering an unprecedented opportunity to unravel sediment facies distribution and localization of anthropogenic disturbance. Finally, the shelf area was ranked, based on the coexistence of multiple stressors from human-driven physical harm, thus providing a semi-quantitative analysis of environmental damage classification in the area.