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The present paper is devoted to the chemical composition analysis of Neogene-quaternary and Paleogene groundwater widely used for drinking in the territory of Tomsk region. It has been shown that groundwater under study contains iron and manganese in excessive concentration. Consequently, this water can negatively affect human health. The ecological and human health risk assessment of Tomsk region groundwater used for drinking has been conducted. According to the calculations, it has been defined that in the overwhelming majority of cases there is a great risk to use groundwater of Tomsk region for drinking purposes.