Coastal systems are among the most studied, most vulnerable, and economically most important ecosystems on Earth; nevertheless, little attention has been paid, so far, to the consequences of human activities on the shallow sea-floor of these environments. Here, we present a quantitative assessment of the effects of human actions on the floor of the tidal channels from the Venice Lagoon using 2500 kilometres of full coverage multibeam bathymetric mapping. Such extended dataset provides unprecedented evidence of pervasive human impacts, which extend far beyond the well known shrinking of salt marshes and artificial modifications of inlet geometries. Direct and indirect human imprints include dredging marks and fast-growing scours around anthropogenic structures built to protect the historical city of Venice from flooding. In addition, we document multiple effects of ship traffic (propeller-wash erosion, keel ploughing) and diffuse littering on the sea-floor. Particularly relevant, in view of the ongoing interventions on the lagoon morphology, is the evidence of the rapid morphological changes affecting the sea-floor and threatening the stability of anthropogenic structures.