To address the issue of saltwater intrusion in the Qiantang River Estuary significantly affecting water resources utilization, a numerical model for saltwater intrusion capable of simulating tidal bores was constructed. The model was calibrated and validated using two sets of field measurements. The temporal and spatial characteristics of salinity variation in the estuary under changing upstream runoff were analyzed. The results show that during dry seasons, although strong tidal dynamics make it difficult for runoff variations to significantly alter estuarine hydrodynamics, sustained freshwater discharge effectively reduces salinity through cumulative dilution, with the desalination effect decreasing from upstream to downstream. Runoff regulation exerts a rapid and prolonged influence on estuarine salinity, with significant responses emerging within one to two days and persisting far longer than the period of runoff variation. To enhance saltwater suppression efficiency and conserve freshwater resources, it is recommended to increase the suppressing discharge one to two days prior to spring tides and gradually reduce it afterward.