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In Colombia, some studies have identified the presence of <jats:italic>vac<\/jats:italic>A and <jats:italic>cag<\/jats:italic>A genes in environmental samples such as treated, surface, and wastewater, but they have not been evaluated in the Bogot\u00e1 River. For this, the aim of this study was to identify the virulence genotypes of <jats:italic>H. pylori<\/jats:italic> present in samples from the Bogot\u00e1 River and domestic wastewater treatment plants (WWTPs).<\/jats:p><\/jats:sec><jats:sec><jats:title>Materials and Methods<\/jats:title><jats:p>A total of 75 water samples (51 from the Bogot\u00e1 River and 24 from wastewater treatment plants) were collected. The presence of <jats:italic>H. pylori<\/jats:italic> DNA and its virulence genotypes was determined by polymerase chain reaction (PCR).<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>The presence of <jats:italic>H. pylori<\/jats:italic> DNA was demonstrated in 44% (33\/75) of the samples, obtaining 63.6% (21\/33) from the Bogot\u00e1 River and 36.4% (12\/33) from the WWTPs. The most prevalent <jats:italic>H. pylori<\/jats:italic> genotype was <jats:italic>cagA<\/jats:italic> (\u2010) and <jats:italic>vacAm1\/s1\/i1<\/jats:italic> being the most virulent of the <jats:italic>vacA<\/jats:italic> gene.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusions<\/jats:title><jats:p>This is the first study in Colombia that determines the <jats:italic>cagA<\/jats:italic> and <jats:italic>vacA<\/jats:italic> genotypes in surface water and WWTPs, indicating the circulation of virulent genotypes in the population. 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