Organic carbon production, respiration, and calcification alter the CO content of water crossing the Eniwetok windward reef flat. Changes in pH and total alkalinity can be used to partition the CO2 changes into those due to production‐respiration and those due to calcification. Gas transfer across the air‐sea interface is minor.Both a transect visually dominated by a mixture of corals and algae and a transect dominated by an algal turf calcified at an average rate of 4,000 g CaCO3 m−2 yr −1, with no apparent day‐to‐night difference. Although nighttime respiration on both transects was 0.12 g C m−2 hr−1, the algal transect exhibited a much higher daytime net production rate than did the coral‐algal transect (0.72 vs. 0.25 g C m−2 hr−1).Although little particulate CaCO3 was removed from the reef flat during these studies, there has been virtually no net CaCO3 accumulation there over the last several thousand years.