The estuarine turbidity maximum (ETM) in the Yangtze Estuary Delta (YED) is muddy by definition and lacks bottom undulations. However, since 2013, a remarkable change has occurred in the YED. Recent images detected by a multibeam echosounder system, SeaBat 7125, for the first time have confirmed widespread regions of subaqueous dunes in the Yangtze ETM channel. This abnormal change is the result of morphodynamic transformation from the combination of an abrupt decline in sediment supply resulting from the construction of the Three Gorges Dam (TGD) and hydrodynamic changes caused by sea level rise. The latter includes anthropogenic-induced sea level rises (from land subsidence and coastal engineering) of 7–37 cm and a climate-induced sea level rise of 8 cm during the past four decades. Obvious evidence of hydrodynamic changes includes tidal amplification, i.e., a 10–28 cm rise in the tidal range, 42–65 cm rise in the lowest tidal level in the dry season, 45–67 cm rise in the highest tidal level in the flood season and 10–30% increase in the amplitude of the major tidal component. These findings will likely have global implications in formulating strategies to combat the superimposed effects of human interventions and climate change on upstream river and downstream coastal developments.