Observations of storm-induced fluid mud dynamics have been conducted at the North Passage deepwater navigational channel (DNC) of the Yangtze Estuary in October to December 2010, during the occurrence of a cold-air front. The measurement data reveal that just after the critical wind wave event, a large amount of fine sediment was trapped in a state of fluid mud along the channel. The observed thickness of the fluid mud was up to about 1–5m, which caused some significant economic and safety problems for shipping traffic in the Yangtze Delta area. The mechanisms and transport processes of the storm-induced fluid mud are analyzed and presented from the angles of both process-oriented and engineering-oriented methods. With the help of hydrodynamics and wave modeling, it could be inferred that the behavior of the storm-induced fluid mud event mainly depends on the overall hydrodynamic regimes and the exchanges of sediment, which is released by storm-wave agitation from adjacent tidal flats. These sediments are accumulated as fluid mud, and subsequently oscillate and persist at those locations with weaker longitudinal residuals in the river- and tide-dominated estuary. In addition, the downslope transport of fluid mud is also thought to have stimulated and worsened the fluid mud event observed in this study. Our modeling results and observations demonstrate that: (1) the transport of fluid mud is an advective phenomenon determining the central position of fluid mud layer along the channel, and it's also a tidal energy influenced phenomenon controlling the erosion and accumulation of fluid mud; and (2) both suspended particulate matter availability and local residual flow regime are of critical importance in determining the trapping probability of sediment and the occurrence of fluid mud.