Single nanometer sized particles are poorly retained by conventional water treatment methods and are hardly detectable in water samples. The particles present a separate class of pollutants and their transport and fate cannot be studied by tracking bacteria, turbidity, free dyes or ions. Dyed bacteriophages and gold nanoparticles are two novel tools that facilitate the studies of virus transport, adsorption and inactivation. The approach is exemplified in studies of slow and rapid sand filtration, ultrafiltration, chlorination and UV disinfection, performed over the last decade. An analysis of general retention trends points to the interrelation between macroscopic particle characteristics and its retention. A better retention, a higher zeta potential and a shorter residence time are associated with larger viruses. A ratio of virus size to its surface area highlights the importance of diffusion as the transport step and electrostatic interactions as the attachment step.