The presence of large bottom roughness, such as that formed by benthic organisms on coral reef flats, has important implications for the size, concentration, and transport of suspended sediment in coastal environments. A 3 week field study was conducted in approximately 1.5 m water depth on the reef flat at Ningaloo Reef, Western Australia, to quantify the cross-reef hydrodynamics and suspended sediment dynamics over the large bottom roughness (∼20–40 cm) at the site. A logarithmic mean current profile consistently developed above the height of the roughness; however, the flow was substantially reduced below the height of the roughness (canopy region). Shear velocities inferred from the logarithmic profile and Reynolds stresses measured at the top of the roughness, which are traditionally used in predictive sediment transport formulations, were similar but much larger than that required to suspend the relatively coarse sediment present at the bed. Importantly, these stresses did not represent the stresses imparted on the sediment measured in suspension and are therefore not relevant to the description of suspended sediment transport in systems with large bottom roughness. Estimates of the bed shear stresses that accounted for the reduced near-bed flow in the presence of large roughness vastly improved the relationship between the predicted and observed grain sizes that were in suspension. Thus, the impact of roughness, not only on the overlying flow but also on bed stresses, must be accounted for to accurately estimate suspended sediment transport in regions with large bottom roughness, a common feature of many shallow coastal ecosystems.

A laboratory experiment was conducted to investigate the dynamics of cross-shore sediment transport across a fringing coral reef. The aim was to quantify how a highly bimodal spectrum of high-frequency (sea-swell) and low-frequency (infragravity and seiching) waves that is typically present on coral reef flats, influences the various sediment transport mechanisms. The experiments were conducted in a 55. m wave flume, using a 1:15 scale fringing reef model that had a 1:5 forereef slope, a 14. m long reef flat, and a 1:12 sloping beach. The initial 7. m of reef flat had a fixed bed, whereas the back 7. m of the reef and the beach had a moveable sandy bed. Four seven-hour irregular wave cases were conducted both with and without bottom roughness elements (schematically representing bottom friction by coral roughness), as well as for both low and high still water levels. We observed that the wave energy on the reef flat was partitioned between two primary frequency bands (high and low), and the proportion of energy within each band varied substantially across the reef flat, with the low-frequency waves becoming increasingly important near the shore. The offshore transport of suspended sediment by the Eulerian mean flow was the dominant transport mechanism near the reef crest, but a wide region of onshore transport prevailed on the reef flat where low-frequency waves were very important to the overall transport. Ripples developed over the movable bed and their properties were consistent with the local high-frequency wave orbital excursion lengths despite substantial low-frequency wave motions also present on the reef flat. This study demonstrated that while a proportion of the sediment was transported by bedload and mean flow, the greatest contributions to cross-shore transport were due to the skewness and asymmetry of the high and low-frequency waves.