In the face of changing global climate the future of corals reefs is uncertain. High latitude reefs may offer potential refugia for corals under projected increasing sea surface temperatures (SSTs). To understand the reef growth potential of modern high latitude reefs it is first necessary to understand past reef growth and response to climatic and environmental changes. The history of the Great Barrier Reef (GBR) has been shown to be punctuated by a multi-millennial Mid-Holocene reef “turn-off” or initiation hiatus in the Northern and Southern GBR (∼5500–2500 years before present [yr. BP]). Here we present the results of chronologically constrained reef matrix cores from five continental island fringing reefs and coral communities in the Keppel Islands to revaluate the timing, extent and possible drivers of the Mid-Holocene hiatus in the Southern GBR. Earliest initiation occurred at Wedge and Halfway Islands at 7773 ± 19 yr. BP and 7455 ± 20 yr. BP, respectively. Following initiation, vertical reef accretion at Halfway was comparable to previously reported rates for the GBR of ∼3.4 mm yr−1, increasing to ∼8.0 mm yr−1 between 6100 and 5500 yr. BP. Conversely, the coral community at Wedge Island, located closer to mainland terrestrial influence, accreted <1.0 mm yr−1 to 5500 yr. BP after which a 3000-year stratigraphic hiatus is observed. A negative relative sea level oscillation at 5500 yr. BP coincides with the transition of Halfway reef from vertical accretion to lateral progradation and the “turn-off” of the Wedge Island coral community. The reef at Middle Island appears to have initiated in the midst of the Mid-Holocene hiatus period at ∼3500 yr. BP, with vertical accretion at both Middle and Halfway Islands being the highest for the region's history at 12.5 ± 3.3 mm yr−1 and 15.0 ± 6.0 mm yr−1, respectively, between 3500 and 3000 yr. BP. A proposed late-Holocene relative sea level highstand of ∼1 m at ∼2000 yr. BP coincides with the first dates identified at near-shore Divided Island, and the re-initiation of coral growth at Wedge Island, although both showed limited net vertical accretion. These near-shore sites “turned-off” again between 1300 and 900 yr. BP, likely associated with a rapid relative sea level fall. Reef progradation also slowed at Halfway Island and Middle Island after 1200 yr. BP until a recent increase in reef growth at Middle Island since the late 1970's associated with modern increases in average SSTs. Our data suggests that although reef-scale “turn-off” events occurred, there is no evidence for a regional scale hiatus in coral growth or initiation comparable to that found further north on the GBR. A comparison with other Southern and south-Central GBR reef cores suggests that relative sea level oscillations in conjunction with changes to climate, appear to have driven varying, but synchronous, modifications to reefs at 5500, 4600, 2800 and 1200 yr. BP.