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Abstract Seagrass meadows are valued for their ecosystem services, including their role in mitigating anthropogenic CO₂emissions through ‘blue carbon’ sequestration and storage. This study quantifies the dynamics of whole ecosystem metabolism on daily to interannual timescales for an eelgrass (Zostera marina) meadow using in situ benthic O₂flux measurements by aquatic eddy covariance over a period of 11 yr. The measurements were part of the Virginia Coast Reserve Long‐Term Ecological Research study, and covered a relatively stable period of seagrass ecosystem metabolism 6–13 yr after restoration by seeding (2007–2014), a die‐off event likely related to persistently high temperatures during peak growing season in 2015, and a partial recovery from 2016 to 2018. This unique sequence provides an unprecedented opportunity to study seagrass resilience to temperature stress. With this extensive data set covering 115 full diel cycles, we constructed an average annual oxygen budget that indicated the meadow was in metabolic balance when averaged over the entire period, with gross primary production and respiration equal to 95 and −94 mmol O₂m⁻²d⁻¹, respectively. On an interannual scale, there was a shift in trophic status from balanced to net heterotrophy during the die‐off event in 2015, then to net autotrophy as the meadow recovered. The highly dynamic and variable nature of seagrass metabolism captured by our aquatic eddy covariance data emphasizes the importance of using frequent measurements throughout the year to correctly estimate trophic status of seagrass meadows. 

Abstract Seagrass meadows play an important role in “blue carbon” sequestration and storage, but their dynamic metabolism is not fully understood. In a denseZostera marinameadow, we measured benthic O₂fluxes 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 O₂flux, 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 O₂concentration and pCO₂, ranging from 173 to 377 μmol L⁻¹and 193 to 859 ppmv, respectively. This 4.5‐fold variation in pCO₂was observed despite buffering by the carbonate system. Hysteresis in diurnal water column pCO₂vs. O₂concentration was attributed to storage of O₂and CO₂in seagrass tissue, air–water exchange of O₂and CO₂, and CO₂storage in surface sediment. There was a ~ 1:1 mol‐to‐mol stoichiometric relationship between diurnal fluctuations in concentrations of O₂and dissolved inorganic carbon. Our measurements showed no stimulation of photosynthesis at high CO₂and low O₂concentrations, even though CO₂reached 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 CO₂concentrations and more frequent temperature extremes.