Abstract. Ecohydrology and hydropedology are two emerging fields that are interconnected. In this study, we demonstrate stemflow hydrology and preferential water flow along roots in two desert shrubs (H. scoparium and S. psammophila) in the south fringe of Mu Us sandy land in North China. Stemflow generation and subsequent movement within soil-root system were investigated during the growing seasons from 2006 to 2008. The results indicated that the amount of stemflow in H. scoparium averaged 3.4% of incident gross rainfall with a range of 2.3–7.0%, and in S. psammophila stemflow averaged 6.3% with a range of 0.2–14.2%. Stemflow was produced from rainfall events more than 1 mm for both shrubs. The average funneling ratio (the ratio of rainfall amount delivered to the base of the tree to the rainfall that would have reached the ground should the tree were not present) was 77.8 and 48.7 for H. scoparium and S. psammophila, respectively, indicating that branches and stems were fully contributing to stemflow generation and thereby provided considerable amount of water to deep soil layer. Analysis of rhodamine-B dye distribution under the shrubs showed that stemflow entered the soil preferentially along root channels contributing to deep storage and that the depth of stemflow infiltrated increased with increasing incident rainfall amount. Distribution of soil water content under the shrubs with and without stemflow ascertained that stemflow was conducive to concentrate and store water in deep layers in the soil profiles, creating favorable soil water conditions for plant growth under arid conditions. Accordingly there is a clear linkage between aboveground ecohydrology and belowground hydropedology in the desert shrubs, whereby an increase in stemflow would result in an increase in soil hydrological heterogeneity.