Based on MODFLOW-CFPv2, a numerical simulation study was conducted to investigate groundwater flow and solute transport processes in the Qinglongkou karst system under concentrated recharge conditions. By coupling conduit flow and matrix flow, the model successfully simulated the dual interaction mechanisms between conduits and matrix in karst systems. Due to limited measured data in the karst aquifer, the study employed the PEST tool to optimize eight key parameters including the hydraulic conductivity of the matrix continuum and conduit diameter, significantly enhancing model accuracy. Conduit diameter and hydrodynamic conditions are crucial factors that influence solute transport. As the conduit diameter increases, the peak solute concentration decreases, while the transit time prolongs. Karst aquifer systems with smaller conduit diameters are at higher risk of contamination than those with larger conduits. When the conduit inlet flow velocity exceeds a critical threshold (800 m/h), the high pressure differentials drive a portion of solutes from the conduit flow into the surrounding interstices of varying sizes and irregular shapes, where subsequent matrix diffusion creates a long-term contamination risk.