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Understanding the variability in soil hydraulic conductivity in the mountainous headwaters is critical to the modeling of mountainous runoff and the water resources management of river basins, especially in the arid and semiarid areas. In this study, a total of 32 soil profiles with five layers within 0-70cm were sampled under different land cover types: forest, meadow, high coverage grassland (HCG), medium coverage grassland (MCG), and barren land in the upper stream of the Heihe river watershed, Northwest China. Saturated hydraulic conductivity (K-S) was measured for each sample. The vertical variation of K-S and soil hydrological response under different land covers were analyzed. Results show that K-S value in layer 5 was significantly lower than the values of above four layers. K-S decreased in the order of forest, meadow, HCG, MCG, and barren land, corresponding to the degree of vegetation degradation. The K-S decreased with depth under forest, HCG, and barren land, but increased first and then decreased under meadow and MCG. The dominant stormflow paths for different land covers were different: forest was dominated by deep percolation, HCG was dominated by subsurface flow (SSF), meadow was prevailed by Hortonian overland flow and had no SSF, while MCG and barren land were also dominated by Hortonian overland flow, but still formed SSF. This result provides important information for improving the accuracy of mountainous hydrological modeling and, in turn, leading to sustainable management of water resources in the study watershed. Copyright (c) 2016 John Wiley & Sons, Ltd.