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Groundwater management can be effectively implemented by assessment of groundwater vulnerability to pollution. The research was carried out in the Vistula River valley (Poland) in an area of shallow groundwater occurrence, defined as a Groundwater-Dependent Ecosystem area. The goal of this study was to identify the average, maximum, and minimum depths of the groundwater table for variant assessment of groundwater vulnerability to contamination. The variants correspond to the average vulnerability, the vulnerability during hydrogeological drought, and the vulnerability during the flood risk period. Theoretical and effective weights of vulnerability parameters were calculated using the DRASTIC method. Vulnerability maps constructed for the various vulnerability variants and by using different parameter weights show the spatial variability of the individual vulnerability classes. Due to the specifics of this protected area, the expected dependency between vulnerability index and chloride concentrations in the monitoring points was not found. Comparison showed strong dependency of water chemistry and the value of recharge, lithology of aquifer, and unsaturated zone. The research results confirm the need for variant vulnerability assessment to protect against floods or predict the effects of climate change.