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Abstract Coral reefs are essential for the foundation of marine ecosystems. However, ocean acidification (OA), driven by rising atmospheric carbon dioxide (CO₂) threatens coral growth and biological homeostasis. This study examines two Hawaiian coral species—Montipora capitataandPocillopora acutato elevated pCO₂simulating OA. Utilizing pH and O₂microsensors under controlled light and dark conditions, this work characterized interspecific concentration boundary layer (CBL) traits and quantified material fluxes under ambient and elevated pCO₂. The results of this study revealed that under increased pCO₂,P. acutashowed a significant reduction in dark proton efflux, followed by an increase in light O₂flux, suggesting reduced calcification and enhanced photosynthesis. In contrast,M. capitatadid not show any robust evidence of changes in either flux parameters under similar increased pCO₂conditions. Statistical analyses using linear models revealed several significant interactions among species, treatment, and light conditions, identifying physical, chemical, and biological drivers of species responses to increased pCO₂. This study also presents several conceptual models that correlate the CBL dynamics measured here with calcification and metabolic processes, thereby justifying our findings. We indicate that elevated pCO₂exacerbates microchemical gradients in the CBL and may threaten calcification in vulnerable species such asP. acuta, while highlighting the resistance ofM. capitata. Therefore, this study advances our understanding of how interspecific microenvironmental processes could influence coral responses to changing ocean chemistry.