Coastal flooding prevention measures, such as storm-surge barriers, are being widely adopted globally because of the accelerating rise in sea levels. However, their impacts on the morphodynamics of shallow tidal embayments remain poorly understood. Here, we combine field data and modeling results from the microtidal Venice Lagoon (Italy) to identify short- and long-term consequences of flood regulation on lagoonal landforms. Artificial reduction of water levels enhances wave-induced sediment resuspension from tidal flats, promoting in-channel deposition, at the expense of salt marsh vertical accretion. In Venice, we estimate that the first 15 closures of the recently installed mobile floodgates operated between October 2020 and January 2021 contributed to a 12% reduction in marsh deposition, simultaneously promoting a generalized channel infilling. Therefore, suitable countermeasures need to be taken to offset these processes and prevent significant losses of geomorphic diversity due to repeated floodgate closures, whose frequency will increase as sea levels rise further.