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.
Supplementary material to "Technical Note: Novel triple O<sub>2</sub>-sensor aquatic eddy covariance instrument with improved time-shift correction reveals central role of microphytobenthos for carbon cycling in coral reef sands"
