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Solute exchange between the sediment and the water column strongly influences water quality in aquatic ecosystems. Among the techniques available for in situ observation, only aquatic eddy covariance (AEC) can resolve the hourly dynamics of benthic fluxes, but only for few substances like oxygen. In micrometeorology, relaxed eddy accumulation (REA), a technique based on high‐frequency sampling conditioned by current direction, overcomes this limitation. We developed a portable prototype instrumentation platform to transfer REA to the sediment‐water interface of shallow aquatic ecosystems. In order to evaluate the sampling system, we configured the prototype for measuring oxygen fluxes and comparing them to simultaneous AEC measurements. In a river and two artificial lakes, at depths 1–3 m and 0.2 m above the sediment, we measured 15 oxygen flux pairs in fully developed turbulence during 8–15 min periods, ranging from −150 to 50 mmol m−2 day−1. The good agreement between REA and AEC fluxes (R2 = 0.94) shows the reliability of the conditional sampling system. REA represents a promising technique for exploring the sediment contribution to biogeochemical cycles in aquatic ecosystems. Plain Language Summary: Microbial activity at the bottom boundary of aquatic ecosystems, such as lakes, rivers and coastal areas, influences their water quality. Microorganisms decompose organic matter and release nutrients and greenhouse gases to the overlying open water. In shallow aquatic ecosystems, the release from the sediment surface can vary rapidly, especially with currents, but so far, no technique succeeds in monitoring dynamic fluxes at hourly timescales for a broad range of substances. In micrometeorology, relaxed eddy accumulation is a well‐established technique for monitoring the turbulent exchange of all kinds of compounds between land and atmosphere (including gas, aerosols and particles). Air is sampled conditionally for downward or upward motions and accumulated in separate containers. Concentration differences between sample pairs provide information on the fluxes. We developed a portable prototype, transferring this technique to quantify the exchange of nutrients and other compounds at the bottom boundary of shallow aquatic ecosystems. For its evaluation, we adapted the prototype to measure dissolved oxygen fluxes. The agreement of its measurements with fluxes measured by aquatic eddy covariance, our reference, shows the potential of this technique. It can now be used to quantify the exchange of major ions and of other substances including dissolved gases. Key Points: We developed a portable instrumentation platform for measuring benthic fluxes in shallow aquatic environments by relaxed eddy accumulationSimultaneous measurements of dissolved oxygen fluxes by aquatic eddy covariance showed the reliability of the conditional sampling techniqueThis work paves the way for exploring the dynamics of biogeochemical cycles in aquatic ecosystems at hourly time scales [ABSTRACT FROM AUTHOR]