Study regionThe Laochang Karst watershed (LCKW) is located in eastern Yunnan Province, southwestern China. It is the representative karst area affected by coal-mining activities in southwestern China. Study focusIdentifying hydrological processes of multi-layered aquifers in karst watersheds is challenging due to complex natural and anthropogenic processes. This study attempts to clarify the hydrological conceptual model of the LCKW using hydrochemistry and D, O, Sr, S, and C isotopes. New hydrological insights for the regionSurface water and multi-layered groundwater have the hydrochemical types of SO4-Ca·Mg, HCO3·SO4-Ca, and HCO3-Ca. Meteoric water and condensate were the major recharge sources. The main processes dominating hydrochemical compositions consist of sulfide oxidative dissolution, carbonate dissolution, positive cation exchange, and agricultural activities. Elevated SO42− concentration in the mine water, river water and shallow coalbed water mainly originated from the oxidation of pyrite in the coal-bearing strata of the Longtan Formation. whereas the deeper layers and groundwater away from the mines were hardly contaminated by SO42− due to the presence of aquiclude. HCO3− concentrations of surface water and multi-layered groundwater were mainly derived from carbonate dissolution and soil CO2, and mine water was also influenced by atmospheric CO2. Positive cation exchange contributed to increasing Na+ concentration. Agricultural activities contributed NO3−, Cl−, and K+ ions in aquifers, especially near large karst fallout caves. A hydrological model of multi-layered aquifers in the LCKW was built based on the above results. These findings will provide valuable guidance for understanding the hydrological processes of complex karst watersheds worldwide.