This study investigates the role of the averaging period of eddy covariance fluxes on the energy balance ratio and further propagation into water use efficiency dynamics. Application was demonstrated on a maize field considering EC flux data. We found that the time averages of EC fluxes that yield the most effective EBR are at 45 and 60 min. The 30 min averaging period was insufficient to capture low-frequency fluxes. Time averaging of EC fluxes needs to be performed based on crop growth stage.