Seawater pH measurements across different reef settings in Cook’s Bay (Moorea, French Polynesia) taken during October and November 2008 were compared and related to circulation and community composition in the reef flat, fringing reef, lagoon and bay. pH is thus an easy measure of seawater carbonate chemistry, which can be altered by community metabolism. Current velocity and percent cover of coral were greatest across the reef flat, yet no significant difference in seawater pH was found between the algal ridge and the lagoon. However, pH variations were discernible between the surface water from the fringing reef, which had the highest percent cover of algae, and water sampled at depth in the lagoon and bay. This study thus brings a better understanding of pH differences within a reef ecosystem and can serve as a benchmark for monitoring ocean acidification.