Scleratinian corals (hard corals) and their symbiotic algae are the ecological engineers of biodiverse and geological important coral reef habitats. The complex, linked physiological processes that enable the holobiont (coral + algae) to calcify and generate reef structures are consequently of great interest. However, the mechanism of calcification is difficult to study for several reasons including the small spatial scales of the processes and the close coupling between the symbiont and host. In this study, we explore the utility of pH and Ca2+ microelectrodes for constraining the rates and spatial distribution of photosynthesis, respiration, and calcification. The work focuses on vertical profiles of pH and Ca2+ through the coelenteron cavity, a semi-isolated compartment of modified seawater amenable to quantitative interpretation. In two studied species, Turbinaria reniformis and Acropora millepora, Ca2+ concentrations decreased in a roughly linear manner from the mouth to the base of the coelenteron, indicating the primary physiological process affecting Ca2+ concentration is removal for calcification below the coelenteron. In contrast, the H+ concentration remained relatively constant over much of the coelenteron cavity before it increased sharply toward the base of the coelenteron, indicative of proton-pumping from the calcification fluid below. The estimated H+ gradient between the coelenteron cavity and the calcification site was >10 times higher than previously predicted. Consequently, the energy required to export protons from the calcifying fluid was estimated to be ~3 times higher than previously calculated. A one-dimensional reaction-diffusion model was used to interpret the pH profile considering the effects of photosynthesis, respiration, and calcification. This model provided a good fit to the observed pH profile and helped to constrain the rates and spatial distribution of these processes. Our modeling results also suggested that adult corals with deeper polyps may be more sensitive to ocean acidification (OA) because of enhanced difficulty to transport H+ out of the coelenteron and into the surrounding seawater.