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The eddy covariance (EC) technique is a powerful tool for measuring atmospheric exchange rates that was recently adapted by biogeochemists to measure aquatic oxygen fluxes. A review of aquatic biogeochemical EC literature revealed that the majority of studies were conducted in shallow waters where waves were likely present, and that waves biased sensor and turbulence measurements. This review identified that larger measurement heights shifted turbulence to lower frequencies, producing a spectral gap between turbulence and wave frequencies. However, some studies sampled too close to the boundary to allow for a spectral turbulence‐wave gap, and a change in how EC measurements are conducted and analyzed is needed to remove wave‐bias. EC fluxes have only been derived from the time‐averaged product of vertical velocity and oxygen, often resulting in wave‐bias. Presented is a new analysis framework for removing wave‐bias by accumulation of cross‐power spectral densities below wave frequencies. This analysis framework also includes new measurement guidelines based on wave period, currents, and measurement heights. This framework is applied to sand, seagrass, and reef environments where traditional EC analysis resulted in wave‐bias of 7.0% ± 9.2% error in biogeochemical (oxygen and H⁺) fluxes, while more variable and higher error was evident in momentum fluxes (10.5% ± 21.0% error). It is anticipated that this framework will lead to significant changes in how EC measurements are conducted and evaluated, and help overcome the major limitations caused by wave‐sensitive and slow‐response sensors, potentially expanding new chemical tracer applications and more widespread use of the EC technique.

The oxygen concentration in marine ecosystems is influenced by production and consumption in the water column and fluxes across both the atmosphere–water and benthic–water boundaries. Each of these fluxes has the potential to be significant in shallow ecosystems due to high fluxes and low water volumes. This study evaluated the contributions of these three fluxes to the oxygen budget in two contrasting ecosystems, aZostera marina(eelgrass) meadow in Virginia, U.S.A., and a coral reef in Bermuda. Benthic oxygen fluxes were evaluated by eddy covariance. Water column oxygen production and consumption were measured using an automated water incubation system. Atmosphere–water oxygen fluxes were estimated by parameterizations based on wind speed or turbulent kinetic energy dissipation rates. We observed significant contributions of both benthic fluxes and water column processes to the oxygen mass balance, despite the often‐assumed dominance of the benthic communities. Water column rates accounted for 45% and 58% of the total oxygen rate, and benthic fluxes accounted for 23% and 39% of the total oxygen rate in the shallow (~ 1.5 m) eelgrass meadow and deeper (~ 7.5 m) reef site, respectively. Atmosphere–water fluxes were a minor component at the deeper reef site (3%) but a major component at the shallow eelgrass meadow (32%), driven by diel changes in the sign and strength of atmosphere–water gradient. When summed, the measured benthic, atmosphere–water, and water column rates predicted, with 85–90% confidence, the observed time rate of change of oxygen in the water column and provided an accurate, high temporal resolution closure of the oxygen mass balance.