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.