Sediment dynamics are widely recognized as a critical bottleneck for the long-term persistence of seagrass meadows. Recently, sedimentation-enhancing strategies for river deltas and estuaries have been increasingly undertaken such as the Water-Sediment Regulation Scheme (WSRS) in the Yellow River, China, which creates an artificial flow regime and further changes the estuarine sediment dynamics. In this study, we examined the spatiotemporal patterns of sediment dynamics at two intertidal meadows, located at an erosional and depositional site, respectively, at the Yellow River Estuary. Field monitoring and radioisotope dating (137Cs and 210Pb) were conducted to explore their responses to the WSRS on both seasonal and inter-annual scales. The results showed that the seasonal sediment dynamics of the meadows at the depositional site exhibited constant changes, while no detectable change was observed at the erosional site. After the implementation of the WSRS, the annual sedimentation rate increased remarkably at both sites, and the flow-sediment regime indicators with high degree of alteration due to the WSRS, i.e., the date of maximum flow and low/high pulse duration of flow were identified as explanatory variables. This study highlights the importance of linking catchment inputs to the condition of seagrass meadows and informs further studies on seagrass-sediment feedback.