Based on the runoff and sediment discharge data of Datong Station from 1960 to 2020, this study analyzed the seasonal variation, interannual variation, and trends of water and sediment fluxes into the Yangtze Estuary. Additionally, the impact of reduced sediment discharge on estuarine evolution was discussed. The results show that: (1) The annual average runoff is 890.6 × 10⁹ m3, with annual values fluctuating around this multi-year average and no significant long-term trend; (2) The seasonal variation of runoff into the sea is distinct, with runoff from May to October accounting for 70.3% of the annual total; (3) The annual average sediment discharge is 33.5 × 10⁷ tons, and the sediment discharge time series generally exhibits a decreasing trend; (4) Due to reduced sediment flux from the Yangtze River Basin, the river regime of the Yangtze Estuary has changed significantly: estuarine sediment concentration has decreased markedly, the estuary has shifted from a siltation environment to an erosion environment, large-scale erosion has occurred on the subaqueous delta front of the YE, and the sediment supply to estuarine sandbars and the subaqueous delta has undergone a structural “source-sink transformation”.