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Root water uptake (RWU) is a unique process whereby plants obtain water from soil, and it is essential for plant survival. The mechanisms of RWU are well understood, but their parameterization and simulation in current Land Surface Models (LSMs) fall short of the requirements of modern hydrological and climatic modelling research. Though various RWU functions have been proposed for potential use in LSMs, none was proven to be applicable for dryland ecosystems where drought was generally the limiting factor for ecosystem functioning. This study investigates the effect of root distribution on the simulated surface energy fluxes by incorporating the observed vertical root distribution. In addition, three different RWU functions were integrated into the Common Land Model (CLM) in place of the default RWU function. A comparison of the modified model’s results with the measured surface energy fluxes measured by eddy covariance techniques in a Central Asian desert shrub ecosystem showed that both RWU function and vertical root distribution were able to significantly impact turbulent fluxes. Parameterizing the root distribution based on in-situ measurement and replacing the default RWU function with a revised version significantly improved the CLM’s performance in simulating the latent and sensible heat fluxes. Sensitivity analysis showed that varying the parameter values of the revised RWU function did not significantly impact the CLM’s performance, and therefore, this function is recommended for use in the CLM in Central Asian desert ecosystems and, possibly, other similar dryland ecosystems. Copyright (c) 2013 John Wiley & Sons, Ltd.