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.