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The oceans are becoming more acidic due to absorption of anthropogenic carbon dioxide from the atmosphere. The impact of ocean acidification on marine ecosystems is unclear, but it will likely depend on species adaptability and the rate of change of seawater pH relative to its natural variability. To constrain the natural variability in reef-water pH, we measured boron isotopic compositions in a ∼300-year-old massive Porites coral from the southwestern Pacific. Large variations in pH are found over ∼50-year cycles that covary with the Interdecadal Pacific Oscillation of ocean-atmosphere anomalies, suggesting that natural pH cycles can modulate the impact of ocean acidification on coral reef ecosystems.