The aquatic eddy-correlation technique can be used to noninvasively determine the oxygen exchange across the sediment-water interface by analyzing the covariance of vertical flow velocity and oxygen concentration in a small measuring volume above the sea bed. The method requires fast sensors that can follow the rapid changes in flow and the oxygen transported by this flow to calculate the momentary advective flux driven by turbulent motions. In this article, we demonstrate that fast optical oxygen sensors, known as optodes, represent a good alternative to the traditional Clark-type electrochemical microelectrodes for such measurements. Optodes have the advantage over microelectrodes of being insensitive to flow, less susceptible to signal drift, more durable under typical field conditions, less expensive, and repairable. Comparisons of the response times of optodes and microelectrodes to rapid oxygen changes showed that optimized optodes had the same response time (162 ± 66 ms) as the microelectrodes (160 ± 57 ms) and were fast enough to capture the oxygen fluctuations that are relevant for the eddy correlation flux calculations. Side by side comparisons of benthic O2 flux data collected with microelectrode-based eddy correlation instruments and optode-based eddy correlation instruments in freshwater and marine environments showed no significant differences between the measured fluxes. The optodes allow the development of more user-friendly eddy correlation instruments that combine the advantages of non-invasive measurements and integration of fluxes over a large footprint area, using a relatively rugged and less expensive sensor.