Microbial water quality lies in the nexus of human, animal, and environmental health. Multidisciplinary efforts are under way to understand how microbial water quality can be monitored, predicted, and managed. This special collection of papers in the Journal of Environmental Quality was inspired by the idea of creating a special section containing the panoramic view of advances and challenges in the arena of microbial water quality research. It addresses various facets of health-related microorganism release, transport, and survival in the environment. The papers analyze the spatiotemporal variability of microbial water quality, selection of predictors of the spatiotemporal variations, the role of bottom sediments and biofilms, correlations between concentrations of indicator and pathogenic organisms and the role for risk assessment techniques, use of molecular markers, subsurface microbial transport as related to microbial water quality, antibiotic resistance, real-time monitoring and nowcasting, watershed scale modeling, and monitoring design. Both authors and editors represent international experience in the field. The findings underscore the challenges of observing and understanding microbial water quality; they also suggest promising research directions for improving the knowledge base needed to protect and improve our water sources.