Ocean acidification is projected to shift coral reefs from a state of net accretion to one of net dissolution this century. Presently, our ability to predict global-scale changes to coral reef calcification is limited by insufficient data relating seawater carbonate chemistry parameters to in situ rates of reef calcification. Here, we investigate natural trends in carbonate chemistry of the Davies Reef flat in the central Great Barrier Reef on diel and seasonal timescales and relate these trends to benthic carbon fluxes by quantifying net ecosystem calcification (nec) and net community production (ncp). Results show that seawater carbonate chemistry of the Davies Reef flat is highly variable over both diel and seasonal timescales. pH (total scale) ranged from 7.92 to 8.17, <i>p</i>CO<sub>2</sub> ranged from 272 to 542 μatm, and aragonite saturation state (Ω<sub>arag</sub>) ranged from 2.9 to 4.1. Diel cycles in carbonate chemistry were primarily driven by ncp, and warming explained 35% and 47% of the seasonal shifts in <i>p</i>CO<sub>2</sub> and pH, respectively. Daytime ncp averaged 36 ± 19 mmol C m<sup>−2</sup> h<sup>−1</sup> in summer and 33 ± 13 mmol C m<sup>−2</sup> h<sup>−1</sup> in winter; nighttime ncp averaged −22 ± 20 and −7 ± 6 mmol C m<sup>−2</sup> h<sup>−1</sup> in summer and winter, respectively. Daytime nec averaged 11 ± 4 mmol CaCO<sub>3</sub> m<sup>−2</sup> h<sup>−1</sup> in summer and 8 ± 3 mmol CaCO<sub>3</sub> m<sup>−2</sup> h<sup>−1</sup> in winter, whereas nighttime nec averaged 2 ± 4 mmol and −1 ± 3 mmol CaCO<sub>3</sub> m<sup>−2</sup> h<sup>−1</sup> in summer and winter, respectively. Net ecosystem calcification was positively correlated with Ω<sub>arag</sub> for both seasons. Linear correlations of nec and Ω<sub>arag</sub> indicate that the Davies Reef flat may transition from a state of net calcification to net dissolution at Ω<sub>arag</sub> values of 3.4 in summer and 3.2 in winter. Diel trends in Ω<sub>arag</sub> indicate that the reef flat is currently below this calcification threshold 29.6% of the time in summer and 14.1% of the time in winter.