If coral reefs continue to degrade, waves on coastlines may substantially increase, leading to greater coastal erosion.

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.

Sediment produced on fringing coral reefs that is transported along the bed or in suspension affects ecological reef communities as well as the morphological development of the reef, lagoon, and adjacent shoreline. This study quantified the physical process contribution and relative importance of sea‐swell waves, infragravity waves, and mean currents to the spatial and temporal variability of sediment in suspension. Estimates of bed shear stresses demonstrate that sea‐swell waves are the key driver of the suspended sediment concentration (SSC) variability spatially (reef flat, lagoon, and channels) but cannot fully describe the SSC variability alone. The comparatively small but statistically significant contribution to the bed shear stress by infragravity waves and currents, along with the spatial availability of sediment of a suitable size and volume, is also important. Although intratidal variability in SSC occurs in the different reef zones, the majority of the variability occurs over longer slowly varying (subtidal) timescales, which is related to the arrival of large swell waves at a reef location. The predominant flow pathway, which can transport suspended sediment, consists of cross‐reef flow across the reef flat that diverges in the lagoon and returns offshore through channels. This pathway is primarily due to subtidal variations in wave‐driven flows but can also be driven alongshore by wind stresses when the incident waves are small. Higher frequency (intratidal) current variability also occurs due to both tidal flows and variations in the water depth that influence wave transmission across the reef and wave‐driven currents.

Coral reefs generate substantial volumes of carbonate sediment, which is redistributed throughout the reef‐lagoon system. However, there is little understanding of the specific processes that transport this sediment produced on the outer portions of coral reefs throughout a reef‐lagoon system. Furthermore, the separate contributions of currents, sea‐swell waves, and infragravity waves to transport, which are all strongly influenced by the presence of a reef, is not fully understood. Here, we show that in reef‐lagoon systems most suspended sediment is transported close to the seabed and can, at times, be suspended higher in the water column during oscillatory flow transitions (i.e., near slack flow) at sea‐swell wave frequencies, and during the peak onshore oscillatory velocity phase at infragravity wave frequencies. While these wave frequencies contribute to the transport of suspended sediment offshore and onshore, respectively, the net flux is small. Mean currents are the primary transport mechanism and responsible for almost 2 orders of magnitude more suspended‐sediment flux than sea‐swell and infragravity waves. Whilst waves may not be the primary mechanism for the transport of sediment, our results suggest they are an important driver of sediment suspension from the seabed, as well as contributing to the partitioning of sediment grain sizes from the reef to the shoreline. As the ocean wave climate changes, sea level rises, and the composition of reef benthic communities change, the relative importance of mean currents, sea‐swell waves, and infragravity waves is likely to change, and this will affect how sediment is redistributed throughout reef‐lagoon systems.

Flow velocities within coral reefs are greatly reduced relative to those at the water surface. The in-reef flow controls key processes that flush heat, cycle nutrients and transport sediment from the reef to adjacent beaches, all key considerations in assessments of reef resilience and restoration interventions. An analytical framework is proposed and tested with a suite of high-resolution numerical experiments. We demonstrate a single parameter that describes the total coral frontal area explains variation of horizontally averaged velocity within a reef canopy across morphologies, densities, and flow depths. With the integration of existing data of coral cover and geometry, this framework is a practical step towards the prediction of near-bed flows in diverse reef environments.