A model that resolves reef island formation in relation to both reef platform substrate development and mid-Holocene sea-level change is presented for Bewick Island, northern Great Barrier Reef, based on morphostratigraphic analysis and radiometrically dated island sediments and reef corals. On Bewick Island, microatolls record reef-flat development at higher sea level (+1.5 m) by 6500 yr B.P. Island building began on a partially emergent reef flat 5000–4000 yr B.P., when sea level was 0.5 m above present. As sea level fell to its present level, the reef platform process window closed and the island core stabilized. Results present the first unequivocal evidence of island building directly over a reef flat comprising microatolls, and the first detailed model of island formation from the Great Barrier Reef. The model demonstrates that the interplay of sea level and reef surface elevation can vary between sites but their convergence is critical for island initiation. Future trajectories of island change will vary, dependent on the unique relative sea level and substrate depth conditions that govern island formation.