Many coral reef ecosystems experience shifts in benthic community composition from scleractinian corals to algae. However, consequences of such phase shifts on O₂ availability, important for many reef organisms, are unresolved. This study therefore comparatively investigated potential in situ effects of different benthic cover by reef macroalgae and scleractinian corals on water column O₂ concentrations in a Northern Red Sea fringing reef. Findings revealed that mean daily O₂ concentrations at algae-dominated sites were significantly lower compared to coral-dominated sites. Minimum O₂ concentrations were significantly negatively correlated, while diurnal variability in O₂ concentration was significantly positively correlated, with increasing benthic cover by algae. In contrast, no correlation with coral cover was found. These results indicate that shifts from corals to benthic algae may likely affect both in situ O₂ availability and variability. This may be particularly pronounced in reef systems with low water exchange (e.g. closed lagoons) or under calm weather conditions and suggests potential O₂-mediated effects on reef organisms.