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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 (<i>SS</i>) 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 (<i>KJ</i>) 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 (<i>FMK</i>) 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 (<i>SS</i>) index holds implications for semi-quantitatively assessing dynamic groundwater vulnerability by delineating flow patterns.