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The variations of seawater CO2 system and organic and inorganic carbon production of coral reefs were investigated with respect to topographic types and oceanographic settings. Because of dominant carbonate production in coral reef ecosystems, most coral reefs are likely to act as a net or at least a potential CO2 source to the atmosphere. The comparison of the seawater CO2 system parameters (pH, total alkalinity, dissolved inorganic carbon and partial pressure of CO2; pCO2) between a reef lagoon and the surrounding ocean allowed us to evaluate the system-level performance of the carbon cycle in the particular reef system. Surface pCO2 in the lagoons of some atolls and barrier reefs in the western Pacific were consistently higher than those of their offshore
waters. The alkalinity decrease in the lagoon water was attributed to calcification of reef organisms. Reef topography, especially residence time of lagoon water, affects the carbon budget of coral reefs to some extent. The offshore-lagoon differences in pCO2 from several reefs showed a tendency to increase with the longer residence time of reef water. Another important factor controlling carbon turnover in coral reefs is proximity to land: terrestrial carbon and nutrient inputs were clearly observed in the northern Great Barrier Reef lagoon as well as a fringing reef of the Ryukyus. These coastal reefs serve as an active CO2-releasing area due not only to calcification but also to degradation of landderived carbon.