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This paper demarcated the most vulnerable regions within the Poiney sub-basin (Tamil Nadu state in India) with respect to the groundwater quality. An index-based vulnerability assessment was carried out by measuring the physico-chemical variables such as pH, electrical conductivity, total dissolved solids, magnesium, sodium, chloride, sulphate, bicarbonate and fluoride in the pre-monsoon and post-monsoon samples. Water quality index varied across the sub-basin due to differences in the water quality induced by anthropogenic activities related to land use practices and presence of industries. The MT3D engine coupled with visual MODFLOW identified that sulphate released from tanneries and leather factories is the main effluent contaminating the groundwater. Model reveals that both the flow and contaminant transport is towards southeast with maximum and minimum calculated head of 201.82 mg/l and 265.92 mg/l and calculated sulphate concentration of 394.40 mg/l and 46.79 mg/l respectively.