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Large bottom roughness is a characteristic of most coral reef environments and this has been shown to have a substantial impact on hydrodynamic processes in these environments. In this paper, we evaluate suspended sediment concentration (SSC) data as well detailed hydrodynamic data over a coral reef flat in Ningaloo Reef, Western Australia, to understand how this bottom roughness affects these processes. A well-developed logarithmic velocity layer consistently developed above a canopy layer during the experiment. Estimates of bottom stresses from these logarithmic profiles were comparable with estimates obtained directly from turbulent Reynolds stresses, and an order of magnitude greater than those typically reported for sandy beach environments having similar flow. Nevertheless, the sediment grain size distribution of the suspended load was very fine relative to what should be mobilized by these stresses, indicated the large roughness substantially suppressed sediment transport.