Photosynthesis and respiration are the two most relevant processes in aquatic ecology, referred as ecosystem metabolism. Isotopic fractionation during those processes drives the stable isotope ratios of the resulting dissolved oxygen and carbon dioxide. Thus, ecosystem metabolism may be monitored using stable isotope analyses of dissolved gases. Storage of the samples in airtight vials is a standard procedure where immediate analysis is not feasible. Mercury chloride is widely accepted as the best-performing preservative. However, due to its toxicity and environmental hazardousness, its use is restricted in some areas, e.g. Sweden. An alternative inhibitor, preferably less toxic, is therefore needed. While several studies have evaluated alternative preservatives for carbon dioxide in freshwater samples, few have focused on conserving accurate oxygen isotope ratios. To address this gap, we compared the time-dependent performance of silver nitrate, sodium azide, zinc chloride, benzalkonium chloride, and sterile-filtration. Water samples from multiple depths within several lotic water bodies showing various chemical and physical states and productivity patterns were compared over up to one year. Concentration and isotopic ratio of the dissolved gases were measured using highly specialized flow injection GC-IRMS. The findings of this research highlight the influence of different inhibitors on stability of stable isotope ratios providing practical guidance for aquatic ecologists to choose an effective and safe substitute for mercury chloride.