The prevalence of antibiotic resistance in pathogens is an increasing concern to health regulators. Although, the risk of contracting diseases from drinking treated water is relatively low, the presence of bacteria harbouring antibiotic resistance genes in water catchments is still unknown. In Singapore, the microbial community and prevalence of antibiotic resistance genes in water catchments around the island are still unknown. This is important as the rivers and catchment areas are increasingly used for water sports and infection by an antibiotic resistant pathogen can pose a risk to the public. We are interested in developing a diagnostic pipeline to test the water quality for potential pathogens and those that carry antibiotic resistance genes.