Low Isles Reef is the most southerly located of 46 coral reef platforms unique to the inner shelf of the northern Great Barrier Reef Province, Australia, which support both seagrass and mangrove growth. Such reefs develop in areas that are influenced by river flood plumes and where inter-reef sediments are dominated by terrigenous mud. Due to its proximity to the coast and spectacular sand cay, Low Isles Reef has long been a popular tourist destination. Informal reports of decreasing visibility, a decline in hard coral cover, and increases in soft coral and fleshy algae have sparked speculation that agricultural activities in coastal catchments are affecting the reef. Comparison of the modern surface of Low Isles Reef with historical archives, including photographs and surveys dating back to 1928, allows quantification of modern sedimentary processes, rates of change, and factors influencing reef development. Results indicate that the distribution of hard corals is limited by the fact that reef growth has reached sea level and accommodation space has been filled. Carbonate production is limited, with Halimeda and the epiphytic foraminifer Marginopora being the major contributors. The most striking changes on Low Isles Reef coincide with cyclones. High energy conditions associated with storm events generate and redistribute rubble sized material, resulting in the catastrophic infilling of topographic lows and the deposition of sheets of coral shingle along the reef periphery. A dramatic expansion of the area of the reef top covered by mangroves since 1928 reflects the development of a composite shingle ridge along the windward margin, which provides an effective barrier against waves and swells. Subtidal ponds, colonized by reef-dwelling organisms, have been periodically created and destroyed by the movement of coral shingle. We suggest that recent changes on Low Isles Reef largely reflect natural processes associated with a coral reef platform that has reached a mature stage of development.