Previous studies of microbially mediated methane oxidation in oceanic environments have examined the many different factors that control the rates of oxidation. However, there is debate on what factor(s) are limiting in these types of environments. These factors include the availability of methane, O2, trace metals nutrients, the density of cell population, and the influence that CO2 production may have on pH. To look at this process in its entirety, we developed an automated mesocosm incubation system with a Dissolved Gas Analysis System (DGAS) coupled to a myriad of analytical tools to monitor chemical changes during methane oxidation. Here, we present new high temporal resolution techniques for investigating dissolved methane and carbon dioxide concentrations and stable isotopic dynamics during aqueous mesocosm and pure culture incubations. These techniques enable us to analyze the gases dissolved in solution and are nondestructive to both the liquid media and the analyzed gases enabling the investigation of a mesocosm or pure culture experiment in a completely closed system, if so desired.