Bacteriophages, viruses that infect bacteria, coexist with their prokaryotic hosts in activated sludge reactors. They are among the most diverse biological entities in aquatic and terrestrial ecosystems, surviving through predation and horizontal gene transfer and have profound effects on microbial ecosystems everywhere. As microbial ecology is an integral part of any environmental biotechnology process, it is important to understand the factors that affect the microbial ecology composition. Little attention has been paid to the diversity of phages in engineered bioreactors, such as in activated sludge processes (ASPs). Phage treatments have the potential to control environmental wastewater process problems including, but not limited to, foaming in activated sludge plants, sludge dewaterability and digestibility; pathogenic bacteria; and to reduce competition between nuisance bacteria and functionally important microbial populations. These problems affect the treatment process and deteriorate the quality of effluent and sludge. Understanding phage–bacterial dynamics is important for successful application of phage therapy to wastewater problems. In this article, we present some important features of bacteriophages and then summarize the current state of knowledge related to the presence of bacteriophages in engineered bioreactors. Finally, we conclude this article with some future recommendations related to the need to study phages in engineered bioreactors.