Increased terrestrial sediment and nutrient yields are regarded as significant threats to coral reef health. Within the central Great Barrier Reef lagoon, where water quality has reportedly declined since European settlement (since ca. A.D. 1850), inner-shelf reef conditions have purportedly deteriorated. However, the link between reef decline and water-quality change remains controversial, primarily because of a lack of pre-European period ecological baseline data against which to assess contemporary ecological states. Here we present a high-resolution record of reef accretion and coral community composition from a turbid-zone, nearshore reef on the inner shelf of the Great Barrier Reef; the record is based on six radiocarbon date–constrained cores, and extends back to ca. 1200 calibrated yr B.P. Results demonstrate not only the potential for coral communities to initiate and persist in settings dominated by fine-grained terrigenous sediment accumulation, but also that a temporally persistent (but low diversity) suite of corals has dominated the reef-building community at this site for at least the past millennium. Furthermore, the coral assemblages exhibit no evidence of community shifts attributable to post-European water-quality changes. While extrapolation of these findings to other turbid-zone reefs must remain tentative, the study raises important questions about the resilience of inner-shelf reefs that are under terrestrial sediment influence and subject to elevated turbidity conditions, and demonstrates the potential to develop detailed, millennial time scale, coral community records from Holocene reef systems.