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.