Hydrodynamic roughness is a critical parameter for characterizing bottom drag in boundary layers, and it varies both spatially and temporally due to variation in grain size, bedforms, and saltating sediment. In this paper we investigate temporal variability in hydrodynamic roughness using velocity profiles in the bottom boundary layer measured with a high-resolution acoustic Doppler profiler (PCADP). The data were collected on the ebb-tidal delta off Grays Harbor, Washington, in a mean water depth of 9 m. Significant wave height ranged from 0.5 to 3 m. Bottom roughness has rarely been determined from hydrodynamic measurements under conditions such as these, where energetic waves and medium-to-fine sand produce small bedforms. Friction velocity due to current u*c and apparent bottom roughness z0a were determined from the PCADP burst mean velocity profiles using the law of the wall. Bottom roughness kB was estimated by applying the Grant-Madsen model for wave-current interaction iteratively until the model u*c converged with values determined from the data. The resulting kB values ranged over 3 orders of magnitude (10-1 to 10-4 m) and varied inversely with wave orbital diameter. This range of kB influences predicted bottom shear stress considerably, suggesting that the use of time-varying bottom roughness could significantly improve the accuracy of sediment transport models. Bedform height was estimated from kB and is consistent with both ripple heights predicted by empirical models and bedforms in sonar images collected during the experiment.