Biological contaminants (BCs), including but not limited to various pathogens and their endogenous pollutants such as intracellular pathogens and antimicrobial resistance genes (ARGs), are ubiquitously detected in effluent of wastewater and drinking water treatment systems which were originally designed to remove common indicator bacteria, resulting in potential impacts on public health. Although there are many emerging technologies that showing promising antimicrobial effects, few have progressed to the actual water scenarios. It’s crucial to understand the main knowledge gaps and thereby design the future developments to better meet engineering requirements. In this review, we first summarize the performance of conventional water treatment towards BCs removal. Then we showcase the advances of proof-of-concept strategies, including nanotechnology, advanced oxidation process, biological control process and integrated techniques, for BCs control in light of antimicrobial mechanisms, characteristics, proper niches in water treatment, challenges and latest improvements. Further, we proposed a semi-quantitative framework coupling life cycle assessment (LCA) and analytic hierarchy process (AHP) to assess and compare the application potential of representative pilot technologies, in which the antimicrobial effects, economic issues and sustainability are comprehensively considered. For wastewater treatment, non-thermal plasma weights highest among the emerging technologies and outperforms conventional disinfection in terms of efficacy indicators (overall inactivation rate, ARGs removal rate and growth inhibition), but fall behind overall mainly due to more energy input. Bacteriophage-based treatment has the potential to synergistically inactive the persistent pathogens in combination with conventional disinfection, serving as a cost-effective and environmental-friendly supplement. For drinking water treatment, the integrated photocatalytic nanocomposite receives the highest application potential among the emerging technologies and appears to be supplementary or even alternative next-generation disinfectants. This review shares valuable insights to propel the proof-of-concept antimicrobial trials towards industrial procedures.