The diffusion boundary layer (DBL) significantly limits the exchange between sediment and overlying water and therefore becomes a bottleneck of diffusive vertical flux at the sediment-water interface (SWI). Variable DBL thickness and diffusion flux in response to dynamic forcing may influence replenishment of nutrients and secondary pollution in coastal waters. In situ measurements of velocity in the bottom boundary layer (BBL) and oxygen concentration in the DBL were made over an intertidal mudflat, using an acoustic Doppler current and mini profiler. A linear distributed zone in the oxygen profile, the profile slope discontinuity and variance of concentration can be used to derive accurate DBL thickness. Diffusion fluxes calculated from the water column and sediment are identical, and their bias is less than 6%. A numerical model PROFILE is used to simulate the in situ dissolved oxygen profile, and layered dissolved oxygen consumption rates in the sediment are calculated. The DBL thickness (0.10-0.35 mm) and diffusion flux (15.4-53.6 mmol m 2 d 1) vary with a factor of 3.5 during a tidal period. Over an intertidal mudflat, DBL thickness is controlled by flow speed U in the BBL, according to δDBL=1686.1DU 1+0.1 (D is the molecular diffusion coefficient). That is, the DBL thickness δDBL increases with decreasing flow speed U. Changes of diffusion flux at the SWI are caused by variations in the water above the sediment and the turbulent mixing intensity. The diffusion flux is positively related to the turbulent dissipation rate, friction velocity and turbulent energy. Under the influence of dynamics in the BBL, DBL thickness and flux vary significantly. The diffusion boundary layer (DBL) significantly limits the exchange between sediment and overlying water and therefore becomes a bottleneck of diffusive vertical flux at the sediment-water interface (SWI). Variable DBL thickness and diffusion flux in response to dynamic forcing may influence replenishment of nutrients and secondary pollution in coastal waters. In situ measurements of velocity in the bottom boundary layer (BBL) and oxygen concentration in the DBL were made over an intertidal mudflat, using an acoustic Doppler current and mini profiler. A linear distributed zone in the oxygen profile, the profile slope discontinuity and variance of concentration can be used to derive accurate DBL thickness. Diffusion fluxes calculated from the water column and sediment are identical, and their bias is less than 6%. A numerical model PROFILE is used to simulate the in situ dissolved oxygen profile, and layered dissolved oxygen consumption rates in the sediment were calculated. The DBL thi Over an intertidal mudflat, DBL thickness is controlled by flow speed U in the BBL, according to a factor of 3.5. δDBL = 1686.1DU 1 + 0.1 (D is the molecular diffusion coefficient). That is, the DBL thickness δDBL increases with decreasing flow speed U. Changes of diffusion flux at the SWI are caused by variations in the water above the sediment and the turbulent The influence of dynamics in the BBL, DBL thickness and flux varies significantly.