Abstract. Sediment–water oxygen fluxes are widely used as a proxy for organic carbon production and mineralization at the seafloor. In situ fluxes can be measured non-invasively with the aquatic eddy covariance technique, but a critical requirement is that the sensors of the instrument are able to correctly capture the high-frequency variations in dissolved oxygen concentration and vertical velocity. Even small changes in sensor characteristics during deployment as caused, e.g. by biofouling can result in erroneous flux data. Here we present a dual-optode eddy covariance instrument (2OEC) with two fast oxygen fibre sensors and document how erroneous flux interpretations and data loss can effectively be reduced by this hardware and a new data analysis approach. With deployments over a carbonate sandy sediment in the Florida Keys and comparison with parallel benthic advection chamber incubations, we demonstrate the improved data quality and data reliability facilitated by the instrument and associated data processing. Short-term changes in flux that are dubious in measurements with single oxygen sensor instruments can be confirmed or rejected with the 2OEC and in our deployments provided new insights into the temporal dynamics of benthic oxygen flux in permeable carbonate sands. Under steady conditions, representative benthic flux data can be generated with the 2OEC within a couple of hours, making this technique suitable for mapping sediment–water, intra-water column, or atmosphere–water fluxes.

Response time is a central characteristic of sensors measuring solute concentrations. Knowing the response time of the sensor under realistic conditions is critically important when measuring rapid changes, e.g., oxygen concentration fluctuations for aquatic eddy covariance flux calculations. Response times therefore should be determined under conditions that are similar to those the sensor is exposed to when deployed for the actual measurements. This study introduces a new method for quantifying the response time of mini‐ or microsensors measuring solute concentrations in liquids and gases. The method is based on the rapid switching of the supply of two fluids with different oxygen concentration to the sensor without removing the sensor from the fluid flow. The device uses a jet nozzle moved by electromagnetic actuators, and the switching of the calibration fluids is monitored by a reference sensor with a response time < 0.001 s. The functionality of the device is demonstrated for a fast oxygen optode system that consisted of a fiber minioptode connected to an oxygen meter that was read by a data logger. With the setup described here, the method permits reproducible response time measurements with a resolution of 0.01 s ± 0.001 s (SD, n = 60). With this technique, the response time characterization of aquatic sensors can be standardized.

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