To predict coral responses to future environmental changes at the reef scale, the coral polyp model (Nakamura et al. in Coral Reefs 32:779–794, 2013), which reconstructs coral responses to ocean acidification, flow conditions and other factors, was incorporated into a reef-scale three-dimensional hydrodynamic-biogeochemical model. This coupled reef-scale model was compared to observations from the Shiraho fringing reef, Ishigaki Island, Japan, where the model accurately reconstructed spatiotemporal variation in reef hydrodynamic and geochemical parameters. The simulated coral calcification rate exhibited high spatial variation, with lower calcification rates in the nearshore and stagnant water areas due to isolation of the inner reef at low tide, and higher rates on the offshore side of the inner reef flat. When water is stagnant, bottom shear stress is low at night and thus oxygen diffusion rate from ambient water to the inside of the coral polyp limits respiration rate. Thus, calcification decreases because of the link between respiration and calcification. A scenario analysis was conducted using the reef-scale model with several pCO2 and sea-level conditions based on IPCC (Climate change 2013: the physical science basis. Contribution of working group I to the fifth assessment report of the intergovernmental panel on climate change, Cambridge University Press, Cambridge, 2013) scenarios. The simulation indicated that the coral calcification rate decreases with increasing pCO2. On the other hand, sea-level rise increases the calcification rate, particularly in the nearshore and the areas where water is stagnant at low tide under present conditions, as mass exchange, especially oxygen exchange at night, is enhanced between the corals and their ambient seawater due to the reduced stagnant period. When both pCO2 increase and sea-level rise occur concurrently, the calcification rate generally decreases due to the effects of ocean acidification. However, the calcification rate in some inner-reef areas will increase because the positive effects of sea-level rise offset the negative effects of ocean acidification, and total calcification rate will be positive only under the best-case scenario (RCP 2.6). [ABSTRACT FROM AUTHOR]
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