Coral cays are low-lying (typically < 5 m above mean sea level) accumulations of calcareous sediment derived from biota on the adjacent reef. They provide areas of societal refuge and support significant ecosystems and economic services. Although environmental controls on cay development are relatively well understood, the precise links between reef ecology, sediment production, and supply to reef islands are less well constrained. Here we identify the major controls on development of sediment facies on a wave-dominated Holocene reef platform on the northern Great Barrier Reef. Remote-sensing data, field observations, and sedimentological analysis (grain size, composition, and taphonomy) reveal sediment transport pathways critical for the development of a coral cay. Collectively, our data reveal six distinct facies types that are chiefly distinguished by the percentage of gravels (> 2 mm grain size) and the relative abundances of foraminifera and coral grains. Gravelly coral-dominated sediment is concentrated at the reef margins, whereas facies on and around the leeward cay are dominated by the sand-size tests of benthic foraminifera. Mud is absent in reef sediments and reflects the prevailing high-energy wave-dominated setting as well as a paucity of mud producers. Benthic foraminifera tests are the major sediment component, constituting an average proportion of 39% (range: 2–77%). Sediment derived from the skeletal remains of corals (24%, 1–65%), mollusks (15%, 3–30%), Halimeda (14%, 4–36%), and coralline algae (6%, 0–20%) are present in lesser volumes. Foraminifera content is highest (> 40%) on tidally emergent algal pavement, where they live in greatest abundance, and on the cay shorelines, where their tests are deposited and comprise the bulk of beach sand (36–63%). A comparison of the Raine Island data with other exposed modern reefs and platforms of the central and western Pacific shows that occurrence and distribution of facies types is broadly consistent. Beyond these sedimentological data, the taphonomy of foraminifera at Raine Island indicates that tests are vulnerable to destruction due to abrasion when transport and reworking is prolonged. Therefore the foraminifera-rich facies adjacent to and on the cay, disjunct from the source zones, as well as taphonomic evidence, imply that transport from the outer reef flat to the cay must be relatively quick. These short temporal links between ecological source zones and depositional landforms are likely to have important ramifications for the contemporary management of reef-associated landforms (e.g., cays) in the future.