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Seagrass meadows play an important role in “blue carbon” sequestration and storage, but their dynamic metabolism is not fully understood. In a dense Zostera marina meadow, we measured benthic O₂ fluxes by aquatic eddy covariance, water column concentrations of O₂, and partial pressures of CO₂ (pCO₂) over 21 full days during peak growing season in April and June. Seagrass metabolism, derived from the O₂ flux, varied markedly between the 2 months as biomass accumulated and water temperature increased from 16°C to 28°C, triggering a twofold increase in respiration and a trophic shift of the seagrass meadow from being a carbon sink to a carbon source. Seagrass metabolism was the major driver of diurnal fluctuations in water column O₂ concentration and pCO₂, ranging from 173 to 377 μmol L−1 and 193 to 859 ppmv, respectively. This 4.5-fold variation in pCO₂ was observed despite buffering by the carbonate system. Hysteresis in diurnal water column pCO₂ vs. O₂ concentration was attributed to storage of O₂ and CO₂ in seagrass tissue, air–water exchange of O₂ and CO₂, and CO₂ storage in surface sediment. There was a ~ 1:1 mol-to-mol stoichiometric relationship between diurnal fluctuations in concentrations of O₂ and dissolved inorganic carbon. Our measurements showed no stimulation of photosynthesis at high CO₂ and low O₂ concentrations, even though CO₂ reached levels used in IPCC ocean acidification scenarios. This field study does not support the notion that seagrass meadows may be “winners” in future oceans with elevated CO₂ concentrations and more frequent temperature extremes.