A field study was carried out to investigate the seasonal variations in alfalfa (Medicago sativa L.) water use efficiency (WUE) using Eddy Covariance (EC) measured CO2 and H2O fluxes, aiming at optimizing the use of irrigation water under hyper arid conditions. The EC system used for this study was installed on a center pivot-irrigated 50 ha alfalfa field. Results revealed that the net EC estimated CO2 uptake ranged from 65,00 kg ha−1 (in winter) to 21,500 kg ha−1 (in summer). While, H2O flux was 4,147 m3 ha−1 (in winter) and 20,157 m3 ha−1 (in summer). This resulted in an estimated alfalfa WUE of 1.57 and 1.07 kg m−3 for winter and summer seasons, respectively. However, the actual WUE of harvested alfalfa was calculated at 0.70 and 0.71 kg m−3 for winter and summer, respectively. Therefore, attaining an actual crop WUE of 33–55% lower than the EC measurement (i.e. more water losses were due to leaching and deep-percolation processes, as the EC system could only estimate evapotranspiration over agricultural fields) emphasizes the need of precision irrigation practices, which will enable farmers to apply irrigation water and agrochemicals more precisely and site-specifically to match soil and plant status and needs.