Abstract. Direct measurement of carbon and water fluxes at high frequency makes eddy covariance (EC) as the most preferred technique to characterize water use efficiency (WUE). However, reliability of EC fluxes is hinged on energy balance ratio (EBR) and inclusion of low-frequency fluxes. This study is aimed at investigating the role of averaging period to represent EC fluxes and its propagation into WUE dynamics. Carbon and water fluxes were monitored in a drip-irrigated Maize field at 10 Hz frequency and are averaged over 1, 5, 10, 15, 30, 45, 60, and 120 minutes considering daytime unstable conditions. Optimal averaging period to simulate WUE fluxes for each growth stage is obtained by considering cumulative frequency (ogive) curves. A clear departure of EBR from unity was observed during dough stage of the crop due to ignorance of canopy heat storage. Error in representing water (carbon) fluxes relative to the conventional 30 min. average is within ± 3 % (± 10 %) for 10–120 min. averaging and is beyond ± 3 % (± 10 %) for other time-averages. Ogive plots conclude that optimal averaging period to represent carbon and water fluxes is 15–30 min. for 6th leaf and silking stages, and is 45–60 min. for dough and maturity stages. Dynamics of WUE considering optimal averaging periods are in the range of 1.49 ± 0.95, 1.37 ± 0.74, 1.39 ± 0.79, and 3.06 ± 0.69 μmol mmol-1 for the 6th leaf, silking, dough, and maturity stages respectively. Error in representing WUE with conventional 30 min. averaging is marginal (< 1.5 %) except during the dough stage (12.12 %). Our findings can help in developing efficient water management strategies by accurately characterizing WUE fluxes from the EC measurements.