Bacterial metabarcoding analysis by 16S rDNA of five occurrences of mineral waters in Serbia (Torda, Slankamen Banja, Lomnicki Kiseljak, Velika Vrbnica and Obrenovacka Banja) indicated the presence of a high percentage of the Proteobacteria phylum, followed by the Bacteroidetes phylum. The families Rhodobacteraceae, Burkholderiaceae, Pseudomonadaceae, Methylophilaceae and Moraxellaceae were the most dominant in the bacterial flora of the selected occurrences, whereas the most represented genera were Acinetobacter, Pseudorhodobacter, Pseudomonas, Limnohabitans, Massilia, Limnobacter and Methylotenera. The presence of coliform bacteria was not detected. Alpha diversity analysis revealed that Slankamen Banja and Lomnicki Kiseljak were the richest of the selected occurrences, while the mineral waters of Torda, Velika Vrbnica and Obrenovacka Banja were characterized by similar diversity of bacterial communities determined by beta diversity analysis. Physical-chemical analysis revealed the value of total dissolved solids above 1 g/L, as well as elevated concentrations of some metals and non-metals. The research concluded that specific bacteria contribute to the development of biocorrosion and biofouling processes of water intake facilities. In addition, some of these bacteria might be potential indicators of the organic sources of pollution and/or biotechnological natural remediators in the treatment of contaminated waters.