Reef growth patterns and the development of associated environments have been extensively studied from reef deposits from Holocene and previous interglacial highstands. However, reefs that grew during glacial lowstands are comparatively poorly understood. Here we show the formation of reef-flat and back-reef environments following rapid sea-level fall (15–20 mm yr−1 and 20–40 m in magnitude) during the Last Glacial Maximum (LGM) on the present shelf edge of the Great Barrier Reef. Sedimentological and foraminiferal analyses of unconsolidated reef sediments recovered in cores 111–140 m below sea level at Hydrographers Passage during Integrated Ocean Drilling Project (IODP) Expedition 325 reveal the occurrence of a benthic foraminiferal assemblage dominated by the genera Calcarina and Baculogypsina, which is common in modern reef-flat and back-reef environments in the Great Barrier Reef and elsewhere. This assemblage is associated with higher foraminiferal proportions in reef sediments and higher proportions of well-preserved Baculogypsina tests in the same intervals, which also characterize reef-flat environments. Radiocarbon (14C–accelerator mass spectrometry) ages of reef-flat dwelling foraminifers (n = 22), which indicate the time when these foraminifers were alive, are consistent with the timing of the two-step sea-level fall into the LGM as defined by the previously published well-dated coralgal record. This foraminiferal evidence suggests the development of geomorphically mature fringing reefs with shallow back-reef lagoons during the LGM. Our results also imply that back-reef sediment accumulation rates during the LGM lowstand were comparable to those during the Holocene highstand.