To simultaneously elucidate patterns of photosynthesis and respiration in aquatic systems, we developed a new gas-switching system for coupled measurements of dissolved metabolic gases. The methodology involves two gas chromatography columns to perform multiple gas separations. The first example using 24 h bottle incubations in estuarine waters showed a 1:1 molar relationship for the coupling between CO2 and O-2 in closed systems during photosynthesis and respiration. In a second, open system application using depth-stratified sampling on the Louisiana continental shelf, deviations from this 1:1 relationship between CO2 and O-2 were common. In surface waters, depletion of CO2 exceeded excess O-2, likely owing to different gas-exchange rates with the atmosphere. In bottom waters, CO2 accumulation could surpass O-2 losses, indicating anaerobic respiration. At intermediate depths, CO2 and O-2 dynamics followed the 1:1 relationship that was observed in the closed incubations. This approach clearly showed that CO2 and O-2 dynamics were tightly coupled on short-time scales, but anaerobic respiration and physical processes such as gas exchange can lead to strong divergence of CO2 and O-2 stoichiometries. This combined analysis of respiratory gases that is readily achievable with isotope ratio mass spectrometer systems illustrates how oxygen and carbon cycles are coupled and decoupled in aquatic systems.