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Abstract. The aquatic eddy covariance technique stands out as a powerful method for benthic O2 flux measurements in shelf environments because itintegrates effects of naturally varying drivers of the flux such as current flow and light. In conventional eddy covariance instruments, the timeshift caused by spatial separation of the measuring locations of flow and O2 concentration can produce substantial flux errors that aredifficult to correct. We here introduce a triple O2 sensor eddy covariance instrument (3OEC) that by instrument design eliminates theseerrors. This is achieved by positioning three O2 sensors around the flow measuring volume, which allows the O2concentration to be calculated at the point of the current flow measurements. The new instrument was tested in an energetic coastal environment with highly permeablecoral reef sands colonised by microphytobenthos. Parallel deployments of the 3OEC and a conventional eddy covariance system (2OEC) demonstrate thatthe new instrument produces more consistent fluxes with lower error margin. 3OEC fluxes in general were lower than 2OEC fluxes, and the nighttimefluxes recorded by the two instruments were statistically different. We attribute this to the elimination of uncertainties associated with the timeshift correction. The deployments at ∼ 10 m water depth revealed high day- and nighttime O2 fluxes despite the relatively loworganic content of the coarse sediment and overlying water. High light utilisation efficiency of the microphytobenthos and bottom currents increasingpore water exchange facilitated the high benthic production and coupled respiration. 3OEC measurements after sunset documented a gradual transfer ofnegative flux signals from the small turbulence generated at the sediment–water interface to the larger wave-dominated eddies of the overlying watercolumn that still carried a positive flux signal, suggesting concurrent fluxes in opposite directions depending on eddy size and a memory effect oflarge eddies. The results demonstrate that the 3OEC can improve the precision of benthic flux measurements, including measurements in environmentsconsidered challenging for the eddy covariance technique, and thereby produce novel insights into the mechanisms that control flux. We consider thefluxes produced by this instrument for the permeable reef sands the most realistic achievable with present-day technology. 

Abstract. Sediment–water oxygen fluxes are widely used as a proxy fororganic carbon production and mineralization at the seafloor. In situ fluxescan be measured non-invasively with the aquatic eddy covariance technique,but a critical requirement is that the sensors of the instrument are able tocorrectly capture the high-frequency variations in dissolved oxygenconcentration and vertical velocity. Even small changes in sensorcharacteristics during deployment as caused, e.g. by biofouling can result inerroneous flux data. Here we present a dual-optode eddy covarianceinstrument (2OEC) with two fast oxygen fibre sensors and document howerroneous flux interpretations and data loss can effectively be reduced bythis hardware and a new data analysis approach. With deployments over acarbonate sandy sediment in the Florida Keys and comparison with parallelbenthic advection chamber incubations, we demonstrate the improved dataquality and data reliability facilitated by the instrument and associateddata processing. Short-term changes in flux that are dubious in measurementswith single oxygen sensor instruments can be confirmed or rejected with the2OEC and in our deployments provided new insights into the temporal dynamicsof benthic oxygen flux in permeable carbonate sands. Under steadyconditions, representative benthic flux data can be generated with the 2OECwithin a couple of hours, making this technique suitable for mappingsediment–water, intra-water column, or atmosphere–water fluxes.