It is not certain whether coral reefs are sources of or sinks for atmospheric CO 2 . Air-sea exchange of CO 2 over reefs has been measured directly and inferred from changes in the seawater carbonate equilibrium. Such measurements have provided conf licting results. We provide community metabolic data that indicate that large changes in CO 2 concentration can occur in coral reef waters via biogeochemical processes not directly associated with photosynthesis, respiration, calcification, and CaCO 3 dissolution. These processes can significantly distort estimates of reef calcification and net productivity and obscure the contribution of coral reefs to global air-sea exchange of CO 2 . They may, nonetheless, explain apparent anomalies in the metabolic performance of reefs close to land and reconcile the differing experimental findings that have given rise to the CO 2 debate.There is debate as to whether coral reefs are sources of or sinks for atmospheric CO 2 (1-4). They may take up about 2% of the annual anthropogenic production of CO 2 if they are sinks (5) or they may release up to 8% if they are sources (6). Gross productivity on coral reefs is among the highest for natural ecosystems (7) and photosynthesis by reef benthos encourages invasion of CO 2 from the atmosphere by reducing its concentration in overlying seawater. Respiration and formation of reef rock (calcification) have the reverse effect. Although calcification decreases the overall concentration of inorganic carbon in seawater, associated acidification,increases the amount present as dissolved (gaseous) CO 2 . Measurements of organic and inorganic carbon metabolism on different reefs have yielded conflicting data on the direction of the net CO 2 flux (1,8). Metabolism on the Tiahura fringing barrier reef, Moorea, apparently released CO 2 to the atmosphere (8), whereas metabolism on Shiraho Reef, Ishigaki Island, Japan, had apparently the reverse effect (1). Most researchers consider that reefs are a source of CO 2 (2,3,6,8,9). Critics of the Shiraho Reef study argue (i) that the reef must have been dominated by noncalcareous algae that increased the ratio of organic to inorganic carbon metabolism, (ii) that the measurements were not representative of the whole reef, and (iii) that erroneous conclusions were drawn from inadequate data (2, 3). Critics also suggest that insufficient measurements were taken to differentiate changes in the concentration of CO 2 caused by benthic metabolism from natural variability in the CO 2 concentration of seawater flowing onto the reef (2). Overall, these criticisms follow from the general view that coral reefs are sources of CO 2 . The net air-sea flux of CO 2 is thought to be controlled by calcification because the ratio of photosynthesis to respiration on unperturbed reefs over 24 h is considered to be close to unity (10).In March 1996, we made an expedition to Lizard Island, northern Great Barrier Reef, Australia (Fig. 1), to measure changes in the O 2 concentration and pH of seawater flowing across a 300...