For over a century, environmental engineers have attempted to control the prokaryotic community biological wastewater treatment processes, but there is growing interest in both understanding and harnessing the activity of phages in wastewater bioprocesses. While phages are known to be present and abundant, their ecological role, potential benefits, and impacts on wastewater biological processes are not fully understood. Fundamental knowledge on how phages infect host cells from relatively simple pure culture studies alongside environmental studies from marine and soil systems can be used to predict the potential impact of phages in diverse and dynamic wastewater environments. This frontier review is focused on what is known about the molecular mechanisms by which phages infect bacteria and how that could apply to biological process control and operation within wastewater treatment systems. Here, we specifically focus on highlights from studies on the molecular mechanisms that drive lysis and lysogeny within phage cells and the impacts on the dissemination of antibiotic resistance genes and nutrient removal within a biological wastewater process.