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ABSTRACT Deltas are crucial for land building and ecological services due to their ability to store mineral sediment, carbon and potential pollutants. A decline in suspended sediment discharge in large rivers caused by the construction of mega‐dams might imperil deltaic flats and wetlands. However, there has not been clear evidence of a sedimentary shift in the downstream tidal flats that feed coastal wetlands and the intertidal zone with sediments. Here, integrated intertidal/subaqueous sediment samples, multi‐year bathymetries, fluvial and deltaic hydrological and sediment transport data in the Nanhui tidal flats and Nanhui Shoal in the Changjiang (Yangtze) Delta, one of the largest mega‐deltas in the world, were analysed to discern how sedimentary environments changed in response to the operations of the Three Gorges Dam. Results reveal that the coarser sediment fractions of surficial sediments in the subaqueous Nanhui Shoal increased between 2004 to 2021, and the overall grain size coarsened from 18.5 to 27.3 μm. Moreover, intertidal sediments in cores coarsened by 25% after the 1990s. During that period, the northern part of the Nanhui Shoal suffered large‐scale erosion, while the southern part accreted in recent decades. Reduced suspended sediment discharge of the Changjiang River combined with local resuspension of fine‐grained sediments are responsible for tidal flat erosion. This study found that the spatial pattern of grain‐size parameters has shifted from crossing the bathymetric isobaths to being parallel to them. Higher tide level and tidal range induced by sea‐level rise, an upstream increase in bed shear stress and larger waves likely further exacerbated erosion and sediment coarsening in deltaic flats. As a result, this sediment‐starved estuary coupled with sea‐level rise and artificial reclamations have enhanced the vulnerability of tidal flats in Changjiang Delta, this research is informative to the sedimentary shift of worldwide mega‐deltas.