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A sedimentological and stratigraphic study of Low Isles Reef off northern Queensland, Australia was carried out to improve understanding of factors that have governed Late Holocene carbonate deposition and reef development on the inner to middle shelf of the northern Great Barrier Reef. Low Isles Reef is one of 46 low wooded island-reefs unique to the northern Great Barrier Reef, which are situated in areas that lie in reach of river flood plumes and where inter-reef sediments are dominated by terrigenous mud. Radiocarbon ages from surface and subsurface sediment samples indicate that Low Isles Reef began to form at ca 3000 y BP, several thousand years after the Holocene sea-level still-stand, and reached sea-level soon after (within ~500 years). Maximum reef productivity, marked by the development of mature reef flats that contributed sediment to a central lagoon, was restricted to a narrow window of time, between 3000 and 2000 y BP. This interval corresponds to: (i) a fall in relative sea-level, from ~1 m above present at ca 5500 y BP to the current datum between 3000 and 2000 y BP; and (ii) a regional climate transition from pluvial (wetter) to the more arid conditions of today. The most recent stage of development (ca 2000–0 y BP) is characterized by extremely low rates of carbonate production and a dominance of destructive reef processes, namely storm-driven remobilization of reef-top sediments and transport of broken coral debris from the reef front and margins to the reef top. Results of the present study enhance existing models of reef development for the Great Barrier Reef that are based on regional variations in reef-surface morphology and highlight the role of climate in controlling the timing and regional distribution of carbonate production in this classic mixed carbonate–siliciclastic environment.