Evidence shows that in the modern ocean, coral reefs are disappearing, and these losses are tied to climate change. However, research also shows that coral reefs can adapt rapidly to changing conditions leading some researchers to suggest that some reef systems will survive future climate change through adaptation. It is known that there were changes in the area covered by coral reefs in the past. Therefore, it is important to investigate the long-term response of coral reefs to environmental changes and high sea-surface temperatures (SSTs). However, because of diagenetic issues with SST proxies in neritic, metastable carbonate-rich environments, there is an incomplete and sometimes even incorrect understanding of how changes in SSTs affect carbonate reef systems. A good example is the Queensland Plateau offshore northeast Australia next to the threatened Great Barrier Reef. In the Late Miocene, between 11 and 7 Ma, a partial drowning caused the reef area on the Queensland Plateau to decline by ~ 50% leading to a Late Miocene change in platform geometry from a reef rimmed platform to a carbonate ramp. This reef decline was interpreted to be the result of SSTs at the lower limit of the modern reef growth window (20–18 °C). This article presents a new Late Miocene—ased SST record from the Coral Sea based on the TEX86H molecular paleothermometer, challenging this long held view. Our new record indicates warm tropical SSTs (27–32 °C) at the upper end of the modern reef growth window. We suggest that the observed temperatures potentially exceeded the optimal calcification temperatures of corals. In combination with a low aragonite supersaturation in the ocean, this could have reduced coral growth rates and ultimately lowered the aggradation potential of the reef system. These sub-optimal growth rates could have made the coral reefs more susceptible to other stressors, such as relative sea-level rise and/or changes in currents leading to reef drowning. Given that these changes affected coral reefs that were likely adapted to high temperature/low aragonite saturation conditions suggests that reefs that have adapted to non-ideal conditions may still be susceptible to future climate changes due to the interaction of multiple stressors associated with climate change.