The response of subaqueous dunes to the variation of riverine sediment supply in an estuary is rarely reported. Five sets of field measurements of bed sediments and topography were made in the Changjiang estuary, China during dry and flood seasons for the past 9 years. Results show that dunes were mainly three-dimensional (3D) during flood seasons and two-dimensional (2D) dunes during dry seasons. Dunes were also much larger in flood seasons. Dunes mainly occurred within the main channels of the estuary although they extended 11.7 km seaward of their normal extent in the South Channel during dry seasons from 2002 to 2006. This extension of the dune field is likely due to a sharp decline of sediment discharge caused by large reservoirs such as Three Gorges.