Sediments of the Venice Lagoon down to 50 cm depth were investigated to assess sediment texture and metal contamination status, before the construction and activation of the MOSE system, which is intended to prevent the periodical flood events affecting the lagoon and the city of Venice. 380 cores were collected in shallow-water areas of the lagoon, and analysed along their vertical profile to determine grain-size distribution and concentrations of some major and trace elements (Al, As, Cr, Cu, Fe, Hg, Mn, Ni, Pb and Zn), total carbon and organic carbon. Radionuclide analyses (137Cs, 210Pb) were performed on 15 cores in an attempt to establish sediment chronology and determine radionuclide inventories in erosional and depositional areas.On the whole-lagoon scale, strong depletion of particles <31 μm in diameter (from medium silt to clay fractions) was observed in sediments down to 10 cm depth in comparison to deeper layers. This depletion characterised both erosional and depositional areas, and may be caused by increased water dynamics and resuspension of sediment due to anthropogenic activities.The apparent sediment accumulation rate determined with 210Pbxs in depositional areas was estimated at 0.2–0.4 cm y−1. In the majority of cores, 210Pbxs inventories were lower than expected from atmospheric fallout, suggesting its export along with fine particles.The different sediment characteristics in terms of grain-size distribution and organic carbon content observed in the upper layer with respect to the deeper ones reflect the modification of the sedimentary balance in recent years. The loss of fine particles, even from sediments in depositional areas of the northern part of the lagoon, may herald changes in local sediment texture leading to a further depletion of morphodiversity, which in turn may lead to the reduction or loss of important lagoon habitats.On the whole-lagoon scale, the prevalently lithogenic elements (Al, As, Cr, Fe, Mn, Ni) decreased towards the top of the cores, reflecting the depletion of fine particles in the upper sediment layer due to winnowing in non-confined lagoon areas. In contrast, partly anthropogenic elements (Cu, Hg, Pb, Zn) increased up to the subsurface sediment layers (5–10 and/or 10–20 cm) as an effect of increasing pollutant inputs until a certain time in the past. Enrichment Factors (EF) were calculated from 9 cores, comparing concentrations in the “pre-industrial” (>100 years ago) and recent (surface layer, 0–5 cm) sediments. The mostly lithogenic elements were not enriched (EF ˜ 1), whereas the partly anthropogenic elements showed slight (Cu and Pb, EF ˜ 1.2) to significant (Hg and Zn, EF ˜ 2) enrichment. The shallow waters on the landward side (particularly close to freshwater inputs), the area nearby the industrial district of Porto Marghera and a small zone adjacent to the city of Chioggia were identified as the main pollutant accumulation sites. Mercury was the only element potentially harmful for aquatic life. Its concentration in the biologically active surface sediment layer (0–5 cm) exceeded the NOAA Effects Range-Median (ERM) value in 27% of samples, corresponding to 20% of the shallow-water surface area.The collected data set represents a valuable reference for monitoring the impact of the construction and operation of the MOSE system on the sediment features of the Venice Lagoon.