Ocean acidification, via an anthropogenic increase in seawater carbon dioxide (CO2), is potentially a major threat to coral reefs and other marine ecosystems. However, our understanding of how natural short-term diurnal CO2 variability in coral reefs influences longer term anthropogenic ocean acidification remains unclear. Here, we combine observed natural carbonate chemistry variability with future carbonate chemistry predictions for a coral reef flat in the Great Barrier Reef based on the RCP8.5 CO2 emissions scenario. Rather than observing a linear increase in reef flat partial pressure of CO2 (pCO2) in concert with rising atmospheric concentrations, the inclusion of in situ diurnal variability results in a highly nonlinear threefold amplification of the pCO2 signal by the end of the century. This significant nonlinear amplification of diurnal pCO2 variability occurs as a result of combining natural diurnal biological CO2 metabolism with long-term decreases in seawater buffer capacity, which occurs via increasing anthropogenic CO2 absorption by the ocean. Under the same benthic community composition, the amplification in the variability in pCO2 is likely to lead to exposure to mean maximum daily pCO2 levels of ca. 2100 μatm, with corrosive conditions with respect to aragonite by end-century at our study site. Minimum pCO2 levels will become lower relative to the mean offshore value (ca. threefold increase in the difference between offshore and minimum reef flat pCO2) by end-century, leading to a further increase in the pCO2 range that organisms are exposed to. The biological consequences of short-term exposure to these extreme CO2 conditions, coupled with elevated long-term mean CO2 conditions are currently unknown and future laboratory experiments will need to incorporate natural variability to test this. The amplification of pCO2 that we describe here is not unique to our study location, but will occur in all shallow coastal environments where high biological productivity drives large natural variability in carbonate chemistry.