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Hydrological and hydrochemical processes in the critical zone of karst environments are controlled by the fracture‐conduit network. Modelling hydrological and hydrochemical dynamics in such heterogeneous hydrogeological settings remains a research challenge. In this study, water and solute transport in the dual flow system of the karst critical zone were investigated in a 73.5‐km2 catchment in southwest China. We developed a dual reservoir conceptual run‐off model combined with an autoregressive and moving average model with algorithms to assess dissolution rates in the “fast flow” and “slow flow” systems. This model was applied to 3 catchments with typical karst critical zone architectures, to show how flow exchange between fracture and conduit networks changes in relation to catchment storage dynamics. The flux of bidirectional water and solute exchange between the fissure and conduit system increases from the headwaters to the outfall due to the large area of the developed conduits and low hydraulic gradient in the lower catchment. Rainfall amounts have a significant influence on partitioning the relative proportions of flow and solutes derived from different sources reaching the underground outlet. The effect of rainfall on catchment function is modulated by the structure of the karst critical zone (e.g., epikarst and sinkholes). Thin epikarst and well‐developed sinkholes in the headwaters divert more surface water (younger water) into the underground channel network, leading to a higher fraction of rainfall recharge into the fast flow system and total outflow. Also, the contribution of carbonate weathering to mass export is also higher in the headwaters due to the infiltration of younger water with low solute concentrations through sinkholes.