Microbes are crucial to the wastewater treatment plants (WWTPs). WWTPs receive large influxes of microbes and are designed to benefit from microbes to treat wastewater. Recent COVID-19 pandemic emphasized their roles in surveilling and predicting infection dynamics in populations. In an era of outbreaks and adverse environmental problems, understanding wastewater microbiome can contribute to the effective surveillance methods and improved wastewater treatment systems. The research presented here focuses on the wastewater surveillance of SARS-CoV-2, phage and bacterial communities and the spread of antibiotic resistance genes (ARGs). The skimmed milk flocculation (SMF) was found out to be effective in concentrating viral particles. This method was successfully applied to surveil SARS-CoV-2 in wastewater and establish relationships between SARS-CoV-2 concentration and infection dynamics in populations. Moreover, the methods developed here formed a basis to study the dynamics and interactions of phage and bacterial communities and phages’ potential contribution to the antibiotic resistance in WWTPs and antibiotic-exposed bench-scale wastewater treatment systems. A combined metagenomics and qPCR approach was employed to study phage and bacterial communities, their potential interactions, and dynamics and mechanisms of antibiotic resistance in wastewater treatment systems. In full-scale WWTPs, the profiles of bacteriomes, phageomes, potential hosts of phages and resistomes were distinct and their compositions diversities followed very similar trends, indicating a habitat- and community-driven population dynamics. While host-phage dynamics in WWTPs was partly in support of Kill the Winner (KtW) hypothesis. On the other hand, dynamics of phage and host communities were highly connected in bench-scale reactors, supporting KtW hypothesis. ARGs were rarely associated with phages, highlighting the limited contribution of phages to the spread of ARGs. On the contrary, phages were found out to encode auxiliary metabolic genes (AMGs) and infect ARG-carrying bacteria and functional wastewater bacteria, indicating phages potential roles in shaping microbial communities and metabolism. Overall, findings of this study provide insights into the phage-host interactions and dynamics in wastewater treatment systems and highlights the limited contribution of phages to the spread of antibiotic resistance. Phages’ potential applications in microbiome engineering and treatment of bacterial infections seems quite promising considering their interaction with prokaryotic communities.