Eddy-correlation measurements of sediment oxygen uptake rates in aquatic systems are increasingly used to obtain areal-averaged fluxes with a high temporal resolution. Here we discuss the effects of coordinate rotation and averaging time scale for Reynolds decomposition on flux estimates. Using 119 hours of continuous eddy-correlation measurements of sediment oxygen fluxes in an impounded river, we demonstrate that rotation of measured current velocities into streamline coordinates can be a crucial and necessary step in data processing under complex flow conditions in non-flat environments with complex topography. We found that under these conditions neither time series detrending nor coordinate rotation can remove low-frequency velocity variations completely. These variations result in spurious flux contributions and in a pronounced dependence of the derived fluxes on averaging time scales. Application of the planar fit transformation was found to provide an alternative means for transforming measured velocities into streamline coordinates for longer-term observations. The observed sensitivity of estimated fluxes to coordinate transformation and selection of averaging time scale is discussed in the context of the theoretical concepts underlying eddy-correlation measurements and a set of recommendations for planning and analyses of flux measurements are derived.