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Desert ecosystems often structured in two distinct layers of woody and herbaceous plants. Changes in community composition alter the fractional coverage by bare soil, woody and herbaceous plants, with potential effects on water and carbon fluxes. We used eddy covariance measurements and chamber method in two similar shrub-dominated desert communities (Tamarix community and Haloxylon community) to assess inter-and intra-annual variations of ecosystem water use efficiency (EWUE) (where we distinguished whole ecosystem EWUE as EWUEE, and EWUE of shrub and herbaceous layers as EWUEShrub and EWUEHerb) in central Asia. In the Tamarix community, 11 years of carbon and water fluxes showed that years with larger herbaceous cover (referred to as shrub-herb years) had significant higher EWUEE than years with lower herbaceous cover (referred to as shrub years), with the values of 1.07 +/- 0.11 vs. 0.68 +/- 0.03 g C/kg H2O. There was a significant positive correlation between EWUEE and the maximum herbaceous plants cover. In the Haloxylon community, chamber measurements during a shrub year demonstrated that the shrub layer contributed most to the gross ecosystem productivity (GEP) and evapotranspiration (ET) of the system, with the herbaceous layer contributing around 30% at the beginning of the growing season, and decreasing to nearly zero during the middle and at the end of the growing season. The shrub layer EWUEShrub was significant higher than that in the herbaceous layer (EWUEHerb) throughout the growing season (1.82 +/- 0.11 vs. 1.06 +/- 0.32 g C/kg H2O). EWUEShrub was positively correlated with EWUEE, but there was no relationship between EWUEHerb and EWUEE in a shrub year. This study shows that the variability of the herbaceous layer across seasons and years in these desert ecosystems is crucial for predicting water and carbon cycling under ongoing and projected climatic change scenarios in shrub dominated desert ecosystems. (C) 2018 Elsevier B.V. All rights reserved.