Anthropogenic activities and climate change have increased the stress on the world’s estuaries over the past decades. Limited knowledge exists about how estuarine receding responds to human interference, particularly the geomorphic dynamics of channels and sandbars. Here, we evaluate the topographic evolution of the upper Yangtze River Estuary (YRE), the largest branch reach with frequently shifting sandbars, from 1994 to 2019. Our results show that a net channel erosion of 9.59 × 10⁸ m³ occurred in the upper YRE, equivalent to an annual erosion depth of 8.67 cm. On the contrary, sandbars with a large area increased from 47.68 km² to 70.88 km², showing the opposite development of estuarine channels. Reduced riverine sediment supply may have been responsible for the estuarine channel erosion, and river engineering may have contributed to intense erosion in local areas. Also, the engineering projects were likely the main reason for the stability and growth of the sandbars. This study reveals the branching channel–sandbar system of the upper YRE in response to anthropogenic and climatic change forcing. The knowledge gained from this study can be applied to other similar estuarine systems around the world, helping develop sustainable strategies for the utilization and protection of the world’s estuaries and deltas.