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Direct measurement of carbon and water fluxes at high frequencies make eddy covariance (EC) the technique most preferred to characterize water use efficiency (WUE). However, reliability of EC fluxes largely hinges on the energy balance ratio (EBR) and inclusion of low-frequency fluxes. This study is aimed at investigating the role of the averaging period in representing 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 were averaged over 1, 5, 10, 15, 30, 45, 60, and 120 min, considering daytime unstable conditions. The 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 the dough and maturity stages of the crop due to ignorance of canopy heat storage, low-frequency flux losses, and an inadequate averaging period. Deviations in representing water (carbon) fluxes relative to the conventional 30 min average are within ±3 % (±10 %) for 10–120 min averaging and beyond ±3 % (±10 %) for other time averages. Ogive plots show that the optimal averaging period to represent carbon, water, and WUE fluxes is 15–30 min for the sixth leaf and silking stages and is 45–60 min for the dough and maturity stages. Dynamics of WUE considering optimal averaging periods are in the range of μ ± σ: 1.49 ± 0.95, 1.37 ± 0.74, 1.39 ± 0.79, and 3.06 ± 0.69 µmol mmol−1 for the sixth leaf, silking, dough, and maturity stages, respectively. The error in representing WUE by conventional 30 min averaging is marginal (< 1.5 %) throughout the crop period except for the dough stage (12.12 %). We conclude that the conventional 30 min averaging of EC fluxes is not appropriate for representing WUE throughout the crop period. Our findings can help to develop efficient water management strategies by accurately characterizing WUE fluxes from the EC measurements.