Changes in the carbonate chemistry of coral reef waters are driven by carbon fluxes from two sources: concentrations of CO2 in the atmospheric and source water, and the primary production/respiration and calcification/dissolution of the benthic community. Recent model analyses have shown that, depending on the composition of the reef community, the air-sea flux of CO2 driven by benthic community processes can exceed that due to increases in atmospheric CO2 (ocean acidification). We field test this model and examine the role of three key members of benthic reef communities in modifying the chemistry of the ocean source water: corals, macroalgae, and sand. Building on data from previous carbon flux studies along a reef-flat transect in Moorea (French Polynesia), we illustrate that the drawdown of total dissolved inorganic carbon (CT) due to photosynthesis and calcification of reef communities can exceed the draw down of total alkalinity (AT) due to calcification of corals and calcifying algae, leading to a net increase in aragonite saturation state (Ωa). We use the model to test how changes in atmospheric CO2 forcing and benthic community structure affect the overall calcification rates on the reef flat. Results show that between the preindustrial period and 1992, ocean acidification caused reef flat calcification rates to decline by an estimated 15%, but loss of coral cover caused calcification rates to decline by at least three times that amount. The results also show that the upstream–downstream patterns of carbonate chemistry were affected by the spatial patterns of benthic community structure. Changes in the ratio of photosynthesis to calcification can thus partially compensate for ocean acidification, at least on shallow reef flats. With no change in benthic community structure, however, ocean acidification depressed net calcification of the reef flat consistent with findings of previous studies.