Oxygen fluxes are a valued proxy for organic carbon production and mineralization at the seafloor. These fluxes can be measured non-invasively with the aquatic eddy covariance instrument, but the fast, fragile oxygen sensor it uses often causes questionable flux data. We developed a dual-O₂-optode instrument and data evaluation method that allow improved flux measurements. Deployments over carbonate sands in the shallow shelf demonstrate that the instrument can produce reliable oxygen flux data.