Abstract: The tidal barrier at the estuary is a critical hydraulic structure for maintaining irrigation and navigation functions in upstream river sections. However, sedimentation issues caused by marine sediment input are common in estuaries where barriers are constructed in China. Taking the Liuduo South Sluice, the final hub of the Northern Jiangsu Main Irrigation Canal, as an example, this study investigates the effects of changes in the sluice site and gate operation on the scouring and deposition processes in the diversion channel section using a two-dimensional water-sediment numerical model. Results show that a scouring-deposition boundary exists in the downstream section of the current Liuduo South Sluice, with the boundary gradually moving downstream. Severe sedimentation occurs upstream of this boundary (sedimentation thickness up to 3.12 m), while slight scouring is observed downstream (maximum scour depth of 0.06 m). The construction and proper operation of a sediment-blocking sluice downstream of the hub reduce net sediment transport toward the upstream, effectively mitigating sedimentation in the diversion channel. A general scouring trend is observed downstream of the sediment-blocking sluice (scour depth 0–0.05 m), while certain sedimentation occurs upstream (sedimentation height 0–0.5 m). As the location of the sediment-blocking sluice moves further downstream, scouring downstream intensifies, and sedimentation upstream weakens.