Terrigenous sediment accumulation within nearshore marine environments is regarded as a major factor inhibiting carbonate production and coral reef accretion. While recent ecological and geological research into reef development under long-term terrigenous sediment influence questions the overly simplistic nature of such views, understanding of the time scales of reef initiation and growth and the morphodynamics of reef accretion in these settings remains limited. Here we present evidence to support recent suggestions that, once established, rapid reef accretion and progradation is possible, but that the restricted accommodation windows in which such reefs develop often result in short-lived (ephemeral) phases of reef building. Specifically, we describe two discrete periods of reef growth within one small (∼600 m wide) coastal embayment around a high island on the terrigenous sediment–dominated inner shelf of the central Great Barrier Reef, Australia. These reef-building phases occurred at either end of the Holocene sea-level highstand, the first during the late postglacial marine transgression and early highstand (∼6900–4500 calibrated (cal) yr B.P.), the second following the late Holocene regression and stillstand (∼1600 cal yr B.P. to present). An ∼3000 yr hiatus occurred between these events, probably as a function of subtle changes in sea level and associated shoreline morphodynamics.