Understanding tidal dynamics in estuaries is essential for tidal predictions and assessments of sediment transport and associated morphological changes. Most studies on river-tide interaction ignored the influences of morphological evolutions under natural conditions such as the seasonal and interannual variations of river discharge. This study analyzes the multiple-timescale tidal dynamics in the Qiantang Estuary, a macro-tidal estuary in China with an extremely active morphological evolution. A large dataset including water levels at representative stations, river discharges and bathymetries since 1980 has been collected. The results of the analysis show that within a spring-neap cycle, the tidal amplification in the upper estuary is stronger during spring tide than during neap tide. This unexpected behavior is due to the high sediment concentration and the unique longitudinal profile of the estuary. On the seasonal and interannual timescales, the low water levels in the upper estuary depend on the local bathymetrical conditions. Tidal ranges in the upper estuary are larger in the high flow season and years, than in the low flow season and years, due to the erosion at high flow, in contrast to estuaries with less active morphological changes. During low flow season and years, the bed is gradually recovered, the low waters are elevated, and the tidal ranges decrease accordingly. A good relationship exists between the tidal ranges and the depth of the upper estuary. In the lower estuary, the flood dominance increases continuously due to embankment. In the upper estuary, the flood dominance is increased during the high flow periods, explaining the fast sediment input and bed recovery in the post high flow periods. A conceptual model of river-tide-morphology interaction of the estuary is proposed, which is also applicable for other shallow systems.