<p>Nanotechnology has emerged as an advanced, sustainable approach to controlling the spread of waterborne pathogens in aquatic environments, addressing a critical global health challenge that causes millions of deaths each year. Increasing pressures from rapid population growth, industrial expansion, and climate change have heightened the need for innovative, efficient water treatment technologies. Although conventional disinfection methods, such as chlorination and ozonation, remain widely used, their use is often associated with the formation of harmful disinfection by-products (DBPs). These limitations have stimulated interest in nanomaterials as alternative antimicrobial agents. Nanoparticles exhibit strong antimicrobial activity, broad-spectrum effectiveness against viruses, bacteria, and protozoa, and a lower potential for by-product formation than traditional disinfectants. This review comprehensively evaluates nanoparticle classifications, synthesis strategies, and their functional advantages in water and wastewater treatment systems. It further explores the mechanisms underlying nanoparticle-mediated pathogen inactivation and biofilm disruption, while discussing current technological advancements and practical challenges. The limitations of conventional treatment approaches are also addressed in the context of emerging global water stressors. Overall, this review provides an integrated, up—to-date perspective on nanomaterial-based water disinfection and biofilm control, emphasizing the relationship between nanomaterial physicochemical properties and their antimicrobial performance.</p>