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To clarify the distribution pattern of the fault-karst groundwater flow system in the Baotu Spring Basin, Shandong Province, China, and to reveal the controlling mechanisms of groundwater flow and the response characteristics of solute transport, this study focused on the Cambrian-Ordovician carbonate rock distribution area within the basin. Karst water, pore water, and surface water samples were collected, and a comprehensive research approach was employed, integrating hydrochemical analysis, statistical analysis, and numerical simulation based on FEFLOW. The results indicate that calcium ions (Ca²⁺) are the dominant cations in the water bodies of the study area, with bicarbonate ions (HCO₃⁻) and sulfate ions (SO₄²⁻) as the primary anions. The average total dissolved solids (TDS) concentrations of karst water, pore water, and surface water are 570.73 mg/L, 746.96 mg/L, and 507.75 mg/L, respectively. The low coefficient of variation in ion concentrations reflects the overall stability of water quality across the study area. Hydrochemical characteristics are predominantly governed by rock weathering, with negligible influence from evaporation-crystallization processes, while atmospheric precipitation exerts a dilution effect. Calcite and dolomite are in a supersaturated state, whereas gypsum and halite are prone to dissolution. Verification results of the groundwater flow numerical model demonstrate that the selected hydrogeological parameters and source-sink terms are reasonable, enabling accurate characterization of the overall groundwater flow field, which flows from southeast to northwest in the study area. Fault zones significantly complicate groundwater flow paths: the Qianfoshan Fault induces flow-line deflection, while the Chaomidian Fault triggers flow-line convergence due to its high permeability. Using nitrate ions (NO₃⁻) as a tracer, this study confirms that fault permeability coefficient and time exert a significant regulatory effect on solute transport and pollution plume distribution. Under the dominance of fault-controlled permeability mechanisms, the pollution plume’s influence range expands dynamically over time as long as a hydraulic head difference persists. This study systematically clarifies the key evolutionary processes and core controlling factors of the fault-karst groundwater flow system in the Baotu Spring Basin, further enriches the theoretical system of hydrogeological research in karst areas of northern China, and provides reliable theoretical support and practical basis for the refined management of regional water resources, ecological protection, and sustainable development.