Tap water quality is a critical public health concern because microbiological contamination in water distribution systems may pose risks to consumers. Therefore, this study seeks to integrate conventional and molecular approaches. Traditional methods, including the Most Probable Number (MPN) and selective culture media, were used to detect microbial indicators of contamination, while molecular analysis using Polymerase Chain Reaction (PCR) was used to identify Escherichia coli at 5 sites within the city’s water distribution network. Metagenomic analysis was performed at two of the five sites selected based on the consistent presence of microorganisms and resource constraints. Sequencing was used to characterize the broader microbial community that may not be detected by culture-based methods. Traditional analyses revealed the presence of thermotolerant coliforms, suggesting potential fecal contamination, while PCR confirmed the presence of Escherichia coli. Metagenomic analysis identified a diverse bacterial community, with the families Moraxellaceae, Pseudomonadaceae and Enterobacteriaceae among the predominant taxa. The combined use of conventional and molecular methods provided complementary information for assessing tap water quality and bacterial taxa of potential sanitary importance.