Potable water reuse has gained significant attention as the demand for reliable sources of water increase due to population growth, intensive land use, and agriculture. Concurrently, the degradation of water quality and exacerbation of water scarcity due to climate change remains a global issue. California has historically practiced water reuse strategies to offset water demands and have been a model for regulatory action for reuse in the United States. Regulatory water quality monitoring of microbial pathogens is however still limited to traditional culture-based methods. Given recent advances in genomic sequencing technologies, comprehensive profiling of microbial communities within these water treatments systems are now possible. Using shotgun metagenomic sequencing, we characterized the bacterial communities by studying community membership, persistence, and shifts, as well as identified potential pathogens. We also analyzed the functional metagenome of biological treatments (activated sludge and biological activated carbon (BAC) filter) for the biodegradation of aromatic compounds. The structure and composition of the microbial communities of each sample location were found to be significantly different from each other using PERMANOVA (P<0.001), which implicates large community shifts after each successive treatment. In fact, treatment location explained about 89% of the total variation between samples. Major anaerobic bacterial classes Bacteroidia and Clostridia were found to be significantly less abundant in advanced treatments by Mann-Whitney test, p=0.015, 0.030, respectively. Proteobacteria were detected in both conventional and advanced treatment samples. Pathogens were detected in the effluent of nearly all treatments except in RO and UV/AOP effluent, however, indicator bacteria were only detected predominantly in raw sewage. . This result stresses the need for improved water quality monitoring and pathogen detection. The number of pathogens detected in advanced treatment were few, while RO and UV/AOP effluent was not able to produce metagenomes due to insufficient genetic material even after filtering over 100Ls. Thus the final water quality of purified water is expected to be highly sterile. The BAC filter biofilm was enriched with aromatic degradation genes mainly contributed by Rhizobia, specifically genus Bradyrhizobium.