Direct covariance observations of the mean flow Reynolds stress and sonar images of the seafloor collected on a wave‐exposed inner continental shelf demonstrate that the drag exerted by the seabed on the overlying flow is consistent with boundary layer models for wave‐current interaction, provided that the orientation and anisotropy of the bed roughness are appropriately quantified. Large spatial and temporal variations in drag result from nonequilibrium ripple dynamics, ripple anisotropy, and the orientation of the ripples relative to the current. At a location in coarse sand characterized by large two‐dimensional orbital ripples, the observed drag shows a strong dependence on the relative orientation of the mean current to the ripple crests. At a contrasting location in fine sand, where more isotropic sub‐orbital ripples are observed, the sensitivity of the current to the orientation of the ripples is reduced. Further, at the coarse site under conditions when the currents are parallel to the ripple crests and the wave orbital diameter is smaller than the wavelength of the relic orbital ripples, the flow becomes hydraulically smooth. This transition is not observed at the fine site, where the observed wave orbital diameter is always greater than the wavelength of the observed sub‐orbital ripples. Paradoxically, the dominant along‐shelf flows often experience lower drag at the coarse site than at the fine site, despite the larger ripples, highlighting the complex dynamics controlling drag in wave‐exposed environments with heterogeneous roughness.