Channel deepening and narrowing are common anthropogenic modifications in estuaries, but their combined effects on estuarine circulation, stratification, and sediment transport remain insufficiently understood. This study investigates these combined impacts in the North Passage of the Changjiang Estuary, where large-scale deepening and narrowing have significantly altered hydrodynamic and sediment processes. Our analysis demonstrates that channel deepening intensifies estuarine circulation by strengthening the landward near-bed flow, thereby enhancing sediment import. Contrary to initial expectations that narrowing would promote sediment flushing, our results indicate that narrowing increases stratification, steepens along-estuary salinity gradients, and suppresses vertical mixing. Intensified stratification further reinforces estuarine circulation, promoting sediment trapping at the saltwater intrusion limit. Additionally, enhanced tidal pumping driven by increased velocity and suspended sediment concentration gradients extends the estuarine turbidity maximum both upstream and downstream, a process often overlooked in engineered estuaries. These findings challenge conventional assumptions regarding the sedimentary impacts of narrowing, emphasizing instead its critical role in amplifying estuarine circulation and sediment trapping. Our results provide new insights into sediment dynamics in river-dominated estuaries, with significant implications for estuarine management, dredging operations, water quality control, and long-term morphological stability.