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This study develops a currents of removal methodology to examine and quantify the nature of physical transport processes affecting the formation of bioclastic deposits in the Cocos (Keeling) Islands, an Indian Ocean atoll. This approach is based on the hydraulic settling and threshold of entrainment characteristics of bioclastic deposits and measured current energy. Potential mobility (PM) analysis of 157 samples quantifies the proportion of deposits able to be transported in each geomorphic zone. Results show that under mean energy conditions wave-induced currents entrain and transport sediment within the atoll and show that transport of sediment is not solely reliant on storm energy conditions. Gradients of PM values are used to reconstruct sediment transport pathways from the reef flat (85–100% PM), through shallow passages (75–100% PM) to sand aprons (50–75% PM) and shallow (0–20% PM) and deep lagoon (0% PM). Comparison of settling velocity distributions of bed material and sediment retained in sediment trap experiments show that actual mobility levels correspond with PM estimates. Potential mobility analysis also identifies the immobile portions of deposits which increase lagoonward. Constituent analysis of immobile fractions and analysis of settling frequency distributions are used to differentiate the importance of physical and biological processes in the formation of deposits throughout Cocos and identify the role of each geomorphic zone in the transport system. The pattern of sediment is controlled by physical processes between the reef flat, the primary sediment production zone, with sediment transported through the shallow passage conduits to the sand aprons. The formation of shallow and deep lagoon deposits is controlled by autochthonous sediment production and storm deposition. Potential mobility analysis is a powerful tool enabling physical transport processes within bioclastic sedimentary environments to be quantified. The ability to examine an individual deposit's hydraulic behaviour and development also enables depositional processes to be examined at a much finer resolution than previously attempted using conventional textural approaches.