Groundwater vulnerability assessments are vital for protecting valuable resources by revealing susceptibility to contamination. This study developed an enhanced index model to assess the intrinsic vulnerability of a supplied karst aquifer in Qingduo, Henan Province. The model considered the 3-D geological structure and modified indices to account for Northern China’s mild karstification. Emphasizing the absolute infiltration capacity of surface contaminants, the model also integrated the groundwater sources and sinks (SS) index. The vulnerability map revealed that over 60% of the aquifers, including the Qingduo wellfield, exhibited very low to low vulnerability. Conversely, only small areas (<5%) along the Kejing (KJ) fault’s southern wall were classified as highly vulnerable. These findings highlighted the significant role of groundwater flow alongside aquifer conditions. The upward groundwater flow through the Fengmenkou (FMK) faults slowed the downward infiltration of surface contaminants into the lower karst aquifer, effectively reducing vulnerabilities. Lower levels of dissolved lead (Pb) and nitrate (NO₃⁻) in Qingduo groundwater aligned with PI_SSR vulnerability mapping. Sensitivity analysis assessed the results’ sensitivity to index weight assignment. The inclusion of the sources and sinks (SS) index holds implications for semi-quantitatively assessing dynamic groundwater vulnerability by delineating flow patterns.