Accurate estimations for the bed shear stress are essential to predict the erosion and deposition processes in estuaries and coasts. This study used high-frequency in situ measurements of water depths and near-bed velocities to estimate bed shear stress on an open intertidal flat in the Yangtze Delta, China. To determine the current-induced bed shear stress (tc) the in situ near-bed velocities were first decomposed from the turbulent velocity into separate wave orbital velocities using two approaches: a moving average (MA) and energy spectrum analysis (ESA). tc was then calculated and evaluated using the log-profile (LP), turbulent kinetic energy (TKE), modified TKE (TKEw), Reynolds stress (RS), and inertial dissipation (ID) methods. Wave-induced bed shear stress (tw) was estimated using classic linear wave theory. The total bed shear stress (tcw) was determined based on the GranteMadsen waveecurrent interaction model (WCI). The results demonstrate that when the ratio of significant wave height to water depth (Hs/h) is greater than 0.25, tcw is significantly overestimated because the vertical velocity fluctuations are contaminated by the surface waves generated by high winds. In addition, wind enhances the total bed shear stress as a result of the increases in both tw and tc generated by the greater wave height and reinforcing of vertical turbulence, respectively. From a comparison of these various methods, the TKEw method associated with ESA decomposition was found to be the best approach because: (1) this method generates the highest mean index of agreement; (2) it uses vertical velocities that are less affected by Doppler noise; and (3) it is less sensitive to the near-bed stratification structure and uncertainty in bed location and roughness.