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In the surface ocean, microorganisms are both a source of extracellular H₂O₂ and, via the production of H₂O₂ destroying enzymes, also one of the main H₂O₂ sinks. Within microbial communities, H₂O₂ sources and sinks may be unevenly distributed and thus microbial community structure could influence ambient extracellular H₂O₂ concentrations. Yet the biogeochemical cycling of H₂O₂ and other reactive oxygen species (ROS) is rarely investigated at the community level. Here, we present a time series of H₂O₂ concentrations during a 28-day mesocosm experiment where a pCO₂ gradient (400–1,450 μatm) was applied to subtropical North Atlantic waters. Pronounced changes in H₂O₂ concentration were observed over the duration of the experiment. Initially H₂O₂ concentrations in all mesocosms were strongly correlated with surface H₂O₂ concentrations in ambient seawaters outside the mesocosms which ranged from 20 to 92 nM over the experiment duration (Spearman Rank Coefficients 0.79–0.93, p-values < 0.001–0.015). After approximately 9 days of incubation however, H₂O₂ concentrations had increased across all mesocosms, later reaching >300 nM in some mesocosms (2–6 fold higher than ambient seawaters). The correlation with ambient H₂O₂ was then no longer significant (p > 0.05) in all treatments. Furthermore, changes in H₂O₂ could not be correlated with inter-day changes in integrated irradiance. Yet H₂O₂ concentrations in most mesocosms were inversely correlated with bacterial abundance (negative Spearman Rank Coefficients ranging 0.59–0.94, p-values < 0.001–0.03). Our results therefore suggest that ambient H₂O₂ concentration can be influenced by microbial community structure with shifts toward high bacterial abundance correlated with low extracellular H₂O₂ concentrations. We also infer that the nature of mesocosm experiment design, i.e., the enclosure of water within open containers at the ocean surface, can strongly influence extracellular H₂O₂ concentrations. This has potential chemical and biological implications during incubation experiments due to the role of H₂O₂ as both a stressor to microbial functioning and a reactive component involved in the cycling of numerous chemical species including, for example, trace metals and haloalkanes.