In situ floc size and turbulent shear stress were measured together with suspended sediment concentration to investigate the floc properties under changing hydrodynamic forcing over the intertidal mudflat. A tripod system was established in the field for a period of approximately one month, including ~ 6 days of stormy conditions in the middle of the investigation period. Mean floc size exhibited strong temporal variations within a tidal cycle, and inverse relationship was found between mean floc size and shear stress. Suspended sediment concentration (SSC) can modulate the flocculation dynamics when shear stress decreases down to enhancing flocculation. Asymmetrical behaviors of floc sizes between flood and ebb phases were identified, with overall larger floc sizes in flood than in ebb tide under the same shear stresses. Floc structure showed different properties under calm and stormy conditions, and the variable fractal dimension and variable primary particle size were more convincing in simulating the variation of floc effective density with mean floc size during the storm period, which was inferred to be related to the resuspension of bed sediment as well as organic matter. A total of 110 mm bed erosion was measured during the storm, and erosion events occurred only around low water, due to the high current-wave combined bed shear stress and off-shore current. After the storm, ~ 40% of the erosion recovered within one week, and the fast settling of large flocs around high water plays significant role in the deposition process, leading to ~ 60% of the recovery.