<p>The Karst groundwater system affected by coal-mining activities is complicated, hampering the sustainable management of groundwater resources. In this study, hydrochemical methods, multivariate statistical methods, and multi-isotope tracing techniques were integrated to clarify the genesis of the karst groundwater system in the Sichuan Basin, southwestern China. Three clusters of groundwater samples were identified in the study area. The hydrochemical type of Cluster I and Cluster II waters was mainly HCO₃-Ca type, and hydrochemical type of Cluster III water was dominated by HCO₃·SO₄-Ca type. The main processes dominating hydrochemical compositions consist of sulfide oxidative dissolution, carbonate dissolution, positive cation exchange, and human activities. The oxidation of sulfides exposed to air and water during coal mining is the primary source of the elevated SO₄²⁻ concentrations. Positive cation exchange resulted in higher Na⁺ concentrations, and agricultural activities added NO₃⁻, Cl⁻, and K⁺ ions to the aquifers. Atmospheric precipitation was the major recharge source. Groundwater is also influenced by evaporation and mineral dissolution. This study developed a hydrogeological conceptual model for the basin karst groundwater system within coal-mining activities. These findings provide valuable information for the sustainable development of karst groundwater resources.</p>