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 O2 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 O2 were common. In surface waters, depletion of CO2 exceeded excess O2, likely owing to different gas-exchange rates with the atmosphere. In bottom waters, CO2 accumulation could surpass O2 losses, indicating anaerobic respiration. At intermediate depths, CO2 and O2 dynamics followed the 1:1 relationship that was observed in the closed incubations. This approach clearly showed that CO2 and O2 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 O2 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.