The patterns and rates of sediment transport across coral reefs influence numerous ecological and morphological processes, yet these dynamics still remain poorly understood. We investigated rates of sediment transport across a 1:15 scale laboratory model with a 1:5 forereef slope, a fixed reef flat and a movable bed (sand) lagoon and beach. Four seven-hour irregular wave simulations were conducted with and without roughness elements on the forereef and reef flat, and with low and high mean water levels. Hydrodynamic processes were analyzed from 18 surface elevation and 8 velocity measurement stations. Suspended sediment concentration across the reef flat was measured continuously at five locations with fast response optical sensors that were periodically supplemented with direct pump sampling. Within the reef system, low frequency wave motions (both infragravity and very low frequency motions) were comparable and sometimes greater than short period motions that defined the incident wave band. Analysis of the sediment concentration signals and decomposition of velocity moments indicate that lower frequency motions play an increasing role across the reef flat and lagoon in driving sediment suspension and transport.