Understanding the influence of waves on bed shear stress is critical for predicting morphodynamical behaviours in coastal areas. Near-bed flow was measured on the middle and lower intertidal mudflats along the Jiangsu coast, China, using a three-dimensional acoustic velocimeter that collected a 3.5-cm vertical profile at 1mm resolution and sample rate of 25 Hz. On the lower and middle tidal flats, velocities from ~2.5-6 cmab (cm above bed) and ~0-3 cmab were measured, respectively. Current-induced bed shear stresses were calculated from turbulent kinetic energy (TKE) at the 11th measurement layer (i.e., 5.1 cm below the probe) using wave-turbulence decomposition and from a logarithmic fit to the horizontal mean velocity profile (LP). A wave boundary layer extended from the bed up to 3 cmab when the significant wave height was 0.23 m; when it was present the near-bed mean velocity profile was non-logarithmic. Waves suppress the development of a vertical velocity gradient and lead to an overestimation of bed shear stress when calculated using the log profile assumption. The TKE method is more accurate than the LP method when waves are present and measurements are at least partially within the wave boundary layer. Accurate calculation of current-induced bed shear stress depends on probe height and wave conditions.