Abstract Internal waves are widespread in oceans and play an important role in mixing. In this study, we observed some oscillations of pycnoclines that are thought to be caused by internal waves by analyzing the vertical and temporal variations of current speed and density during ebbs of the neap tides in the south channel of the Yangtze River (Changjiang) Estuary. These oscillations have an amplitude of 1–2 m and a duration of 2–3 h. To explore the mechanism of this phenomenon, topographic features of the seabed were recorded, and a huge sandbar was observed at the place where the oscillations occurred. Therefore, we infer the oscillations in the south channel were caused by the process that the stratified water flowed over the sandbar which induced internal hydraulics and led to the excitation of internal waves. Froude number was calculated according to the internal-hydraulics equations and the results verified our hypothesis that it was the interactions between the stratified water and rapidly changing topography that triggered internal hydraulics. Internal waves caused upward-directed water movement, which influenced the vertical transport of sediment and the vertical distribution of the suspended sediment. Internal waves also increased the mass diffusivity coefficient (Kz) at the interface of internal waves.