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Epikarst exerts a strong control on run-off generation in karst regions, but it is still unclear in karst regions. Our study aimed to demonstrate the effect of epikarst on near-surface hydrological processes in a subtropical cockpit karst region of southwest China, using plot-scale rainfall simulation experiments with different rainfall intensities (low and high) and antecedent moisture conditions (dry and wet). A trench excavated to the epikarst lower boundary allowed identification of flow pathways in the entire soil–epikarst architecture system, thus facilitating the water balance calculations using a conceptual model with the assumption of a two-stage hydrological evolution. More than 70% of the total rainfall water moved vertically through the shallow soil layer and then was redistributed by the epikarst as subsurface flow occurring on the soil–epikarst interface, depression filling on epikarst surface, water held by epikarst and deep percolation. Epikarst water regulation capacity, defined as the sum of depression filling on epikarst surface, water held by epikarst, epikarst seepage flow and deep percolation, was 58 mm (wet antecedent condition) and 223 mm (dry antecedent condition). Total run-off from the soil–epikarst system was dominated by saturated subsurface flow showing a threshold process controlled by epikarst storage capacity (storing as much as 181 mm of rainfall water under dry antecedent condition). Our study proved that despite the epikarst being relatively poorly developed and covered by a soil mantle, it still exerted a strong influence on near-surface hydrological processes and thus should be adequately considered in future modelling of water recharge and depletion dynamics in this integrated soil–epikarst system. Copyright © 2015 John Wiley & Sons, Ltd.