Reviews suggest that that the biogeochemical threshold for sustained coral reef growth will be reached during this century due to ocean acidification caused by increased uptake of atmospheric CO2. Projections of ocean acidification, however, are based on air-sea fluxes in the open ocean, and not for shallow-water systems such as coral reefs. Like the open ocean, reef waters are subject to the chemical forcing of increasing atmospheric pCO2. However, for reefs with long water residence times, we illustrate that benthic carbon fluxes can drive spatial variation in pH, pCO2 and aragonite saturation state (Ωa) that can mask the effects of ocean acidification in some downstream habitats. We use a carbon flux model for photosynthesis, respiration, calcification and dissolution coupled with Lagrangian transport to examine how key groups of calcifiers (zooxanthellate corals) and primary producers (macroalgae) on coral reefs contribute to changes in the seawater carbonate system as a function of water residence time. Analyses based on flume data showed that the carbon fluxes of corals and macroalgae drive Ωain opposing directions. Areas dominated by corals elevate pCO2 and reduce Ωa, thereby compounding ocean acidification effects in downstream habitats, whereas algal beds draw CO2 down and elevate Ωa, potentially offsetting ocean acidification impacts at the local scale. Simulations for two CO2 scenarios (600 and 900 ppm CO2) suggested that a potential shift from coral to algal abundance under ocean acidification can lead to improved conditions for calcification in downstream habitats, depending on reef size, water residence time and circulation patterns. Although the carbon fluxes of benthic reef communities cannot significantly counter changes in carbon chemistry at the scale of oceans, they provide a significant mechanism of buffering ocean acidification impacts at the scale of habitat to reef.