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Hydrological processes in karst basins are controlled by permeable multimedia, consisting of soil pores, epikarst fractures, and underground conduits. Distributed modelling of hydrological dynamics in such heterogeneous hydrogeological conditions is a challenging task. Basing on the multilayer structure of the distributed hydrology-soil-vegetation model (DHSVM), a distributed hydrological model for a karst basin was developed by integrating mathematical routings of porous Darcy flow, fissure flow and underground channel flow. Specifically, infiltration and saturated flow movement within epikarst fractures are expressed by the ‘cubic law’ equation which is associated with fractural width, direction, and spacing. A small karst basin located in Guizhou province of southwest China was selected for this hydrological simulation. The model parameters were determined on the basis of field measurement and calibrated against the observed soil moisture contents, vegetation interception, surface runoff, and underground flow discharges from the basin outlet. The results show that due to high permeability of the epikarst zone, a significant amount of surface runoff is only generated after heavy rainfall events during the wet season. Rock exposure and the epikarst zone significantly increase flood discharge and decrease evapotranspiration (ET) loss; the peak flood discharge is directly proportional to the size of the aperture. Distribution of soil moisture content (SMC) primarily depends on topographic variations just after a heavy rainfall, while SMC and actual ET are dominated by land cover after a period of consecutive non-rainfall days. The new model was able to capture the sharp increase and decrease of the underground streamflow hydrograph, and as such can be used to investigate hydrological effects in such rock features and land covers. Copyright © 2011 John Wiley & Sons, Ltd.