Human interventions influence sediment dynamics, and understanding these mechanisms is essential for predicting short-term and long-term estuarine development. The Deep Channel Navigation Project (DCNP) in the Yangtze Estuary is such a large infrastructural intervention that substantially alters sediment exchanges between channels and shoals and may thereby influence this estuarine development. However, the effect of these constructions on channel-shoal sediment exchange is up to now poorly known. In this study, we use an extensive dataset collected both in channels and on shoals and a numerical model to clarify the exchange mechanisms driving sediment transport patterns in a strongly anthropogenically modified environment. The results indicate that the stepwise construction of hydraulic structures leads to gradual changes in sediment exchange. The first phase was characterized by partially blocked sediment exchange with northward sediment transport towards the main channel and to the northern flats (2002–2010). Next, a transition period was characterized by weaker horizontal sediment exchange and reduced sediment supply (2010–2016). Since 2016, more efficient structures blocking sediment exchange further hinder northward transport and promote deposition on the southern flats. These processes point to the important role of engineering works in strengthening the southward growth of the delta. Moreover, data analyses suggest that northward over-jetty flow during high water induces a net sediment flux towards the channel due to water level gradients. The residual flow controls the net sediment transport both in the longitudinal and lateral direction over the tidal flats. Therefore, a clockwise residual circulation cell forms in the channel-shoal system, contributing to the channel siltation. These findings shed important insights into the role of sediment exchange in channel siltation and large-scale hydrodynamic and delta development. Such knowledge is crucial for sustainable future management of delta distributaries.