Short-term bed-level variability in tidal wetlands has important implication both for ecology and engineering. In this study, we combined in situ measurements with model simulations to quantify short-term bed-level changes on a meso-macrotidal wetland in the Yangtze River Delta. On the middle flat, we observed erosion during neap-to-mean tides under onshore moderate-to-strong winds, and bed recovery during subsequent spring tides, when winds were both offshore and weaker, suggesting that winds can overturn the neap–spring cyclicity of bed-level changes even on meso–macrotidal mudflats. The magnitude of bed-level changes was smaller on both sides of the middle flat, while the smallest changes occurred on the salt marsh. Observed bed-level changes were reconstructed using a single-point bed-level change model, which incorporates in situ measured parameters of hydrodynamics (waves and currents), suspended sediment concentrations, and bed sediment properties. We conclude that the relative importance of waves and tides in intertidal wetland erosion and accretion can vary temporally (due to changes in balance between wave and tidal energies) and spatially (because of changes in elevation and vegetation in the cross-shore profile). Our study also reflects the advantage of combination of in situ measurement with simulation in detecting short-term variability of tidal flats.