Eddy covariance measurements have become a widespread method in atmospheric sciences to determine scalar fluxes a long time ago. Due to its non-invasiveness and the fact that it integrates over a larger surface areas and therefore includes the heterogeneity of the investigated site, it is considered a promising approach also for aquatic systems. Still, eddy correlation measurements in aquatic systems have not been applied very frequently and are still far away from becoming a standard method. First successful attempts to measure sediment fluxes of oxygen as well as sediment bed erosion have been reported about 15 years ago. One of the reasons for the late and slow establishment of the eddy correlation method in aquatic sciences is the lack of suitable sensors for the scalar measurements which require a response time which is fast enough to resolve the lowest timescales of flux contributing eddies. On the other hand, the investigated aquatic systems themselves pose challenges. In order to determine reasonable sedimentary oxygen uptake rates, sufficiently persistent turbulent periods are required. Normally, these conditions prevail in rivers and tidal systems, while they are generally not encountered in lakes and data from these systems need to be interpreted carefully. On the other hand, especially shallow marine systems are frequently affected by waves which interfere with the turbulence signal. In our talk, we will present our experience with the aquatic eddy correlation over the last 10 years and provide an outlook on how to tackle some of the remaining challenges.