This study evaluated the microbiological safety of the water distribution system of a city in the state of Minas Gerais (Brazil), population 120,000 inhabitants. During the study, the city suffered a severe drought that had a significant impact on water availability and quality in the river that supplies water to the city. Samples (2 liters) were collected from the distribution system over a period of six months, which included wet and dry months, from three points: the point with the lowest altitude in the distribution network, the farthest point from the water treatment works, and an intermediate point. Free chlorine was measured in situ using a Hach kit. DNA was extracted using a FastDNA Spin Kit Soil (Qbiogene). Advanced sequencing techniques (Ion Torrent) were used to identify and quantify the relative abundance of potentially pathogenic bacteria present in the samples. Coliforms and Escherichia coli, indicators currently used worldwide to assess microbiological safety of drinking water, were measured on all samples using an enzyme substrate method (ONPG-MUG Colilert®). Next generation sequencing results retrieved 16SrRNA sequences of E. coli and some potentially pathogenic bacteria, even in the presence of free chlorine. Operational taxonomic units related to pathogenic bacteria were present in all samples from the drinking water distribution system (DWS) and, in general, at high relative abundance (up to 5%). A total of 19 species related to bacterial pathogens were detected. Inadequate operational practices that could affect the microbiological safety of the DWS were identified and discussed. The current paper is the first to evaluate the community of potentially pathogenic bacteria in a real DWS.