The emergence of next generation sequencing (NGS) is revolutionizing the potential to address complex microbiological challenges in the water industry. NGS technologies can provide new and holistic insight into microbial communities and their functional capacities in water and wastewater systems, thus eliminating the need to develop a new assay for each target organism or gene. This project advances the application of NGS in the water industry by documenting the current state-of-the-science of NGS technologies, identifying key knowledge gaps and barriers to their implementation, validating relevant approaches, and developing a guidance document to aid water professionals in navigating options for NGS applications. Research partner: California State Water Resources Control Board. Published in 2023.