Acidification of the oceans by increasing anthropogenic CO2 emissions will cause a decrease in biogenic calcification and an increase in carbonate dissolution. Previous studies have suggested that carbonate dissolution will occur in polar regions and in the deep sea where saturation state with respect to carbonate minerals (Ω) will be <1 by 2100. Recent reports demonstrate nocturnal carbonate dissolution of reefs, despite a Ωa (aragonite saturation state) value of >1. This is probably related to the dissolution of reef carbonate (Mg-calcite), which is more soluble than aragonite. However, the threshold of Ω for the dissolution of natural sediments has not been clearly determined. We designed an experimental dissolution system with conditions mimicking those of a natural coral reef, and measured the dissolution rates of aragonite in corals, and of Mg-calcite excreted by other marine organisms, under conditions of Ωa > 1, with controlled seawater pCO2. The experimental data show that dissolution of bulk carbonate sediments sampled from a coral reef occurs at Ωa values of 3.7 to 3.8. Mg-calcite derived from foraminifera and coralline algae dissolves at Ωa values between 3.0 and 3.2, and coralline aragonite starts to dissolve when Ωa = 1.0. We show that nocturnal carbonate dissolution of coral reefs occurs mainly by the dissolution of foraminiferans and coralline algae in reef sediments.