This partnership between the University of São Paulo and the University of Sheffield is dedicated to tackling microbial challenges within drinking water systems. Microorganisms present in drinking water are a substantial threat to public health, as they can lead to waterborne diseases, antimicrobial resistance, and the generation of harmful by-products. Effective management of outbreaks related to waterborne diseases needs a comprehensive understanding of the mechanisms governing pathogen dynamics. Through the application of metagenomics, which involves studying genes and genomes in environmental samples, we can uncover the presence and activities of microbes associated with failures and deficiecies in drinking water systems. Our objective is to introduce innovative approaches and expertise to enhance management strategies in urban water systems.