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In the Venetian lagoon, the storm surge barriers (Mo.S.E. system) are crucial to prevent urban flooding during extreme stormy events. The inlet closures have some cascading effects on the hydrodynamics and sediment transports of this shallow tidal environment. The present study aims at investigating the effects of the Mo.S.E. closure on the wind-wave propagation inside the lagoon. In situ wave data were collected to establish a unique dataset of measurements recorded in front of San Marco square between July 2020 and December 2021, i.e., partially during the COVID-19 pandemic. Ten storm events were analyzed in terms of significant wave heights and simultaneous wind characteristics. This dataset allowed for validating a spectral wave model (SWAN) applied to the whole lagoon. The results show that the floodgate closures, which induce an artificial reduction of water levels, influence significant wave heights <i>H</i>_S, which decrease on average by 22% compared to non-regulated conditions, but in the shallower areas (for example tidal flats and salt marshes), the predicted decrease is on average 48%. Consequently, the analysis suggests that the Mo.S.E. closures are expected to induce modifications in the wave overtopping, wave loads and lagoon morphodynamics.