A comparison of 1927, 1970 and 2002 bathymetric surveys in the Lagoon of Venice was used to reconstruct historical changes in sedimentation. A detailed GIS-based analysis of the charts revealed the timing and pattern of geomorphic changes and allowed calculation of sediment deposition and erosion for the entire lagoon and each of its four sub-basins: Treporti, Lido, Malamocco and Chioggia. Two main developments are discernible from comparative observation of the areal distribution of the main elevation ranges: the diminution in area of the saltmarshes, which decreased by more than 50%, from 68 km 2 in 1927 to 32 km 2 in 2002, and the progressive deepening of the lagoon, with a huge increase in the area of subtidal flats (between −0.75 and −2.00 m depth), from 88 to 206 km 2 during the same period. Generally, the lagoon showed a clear-cut change in the most frequent depths (modal depth) from a value of −0.62 m in 1927 to −0.88 m in 2002. The deepening of the lagoon affected mostly the lagoonal sub-basins south of the town of Venice, where modal depth increased from −0.65 to −1.12 m in Lido, from −0.64 to −1.75 m in Malamocco and from −0.39 to −0.88 m in Chioggia. Large changes in lagoonal morphology were caused by human-induced subsidence, the dredging of navigation channels between 1927 and 1970, and intense natural erosion enhanced by sediment re-suspension due to Manila clam fishing between 1970 and 2002. There was a net loss of about 110 Mm 3 of sediment from the lagoon, most of which (73 Mm 3, ca.70%) was in the earlier period. A significant amount was lost by dredging and direct disposal outside the system, either on land or at sea, and there was a net loss of 39 Mm 3 from the lagoon to the sea through the inlets, at an annual rate of 0.5 Mm 3. Comparison of erosion rates in the two periods revealed an alarming acceleration, from a net sediment loss of 0.3 Mm 3 yr −1 in the period 1927–1970 to 0.8 Mm 3 yr −1 in 1970–2002. Deterioration caused a shift from a highly differentiated lagoon morphology in the 1930s to a sediment-starved and subsidence-dominated structure in the 1970s, and from there to the high-energy and more open (bay-like) lagoon of today. The results demonstrate the potential application of GIS to reconstruct the recent chronology of sediment distribution and to improve the understanding of the geomorphic processes shaping the seafloor, whilst providing an insight into the possible impacts of environmental changes induced by natural and anthropogenic forcing.