Human viruses are widespread in the water environment and pose a risk to human health. Wastewater effluents represent the main source of viruses discharge in the environment, leading to contamination of aquatic ecosystems. Viral pathogens can persist on the long- term in these ecosystems and cause human viral infections via water or food. Many studies on inactivation of viruses using UV, heat or chlorine have been conducted. However, the control of viruses by microorganisms, such as bacteria and protists, has only been partially studied. The removal or inactivation of viruses by grazers is a challenging field of study as this natural process might be exploited to engineer water treatment biological solutions. My thesis aims at understanding by which mechanisms, and under which conditions, protists control human viral pathogens, and to design or improve water treatment solutions based on microbial control of viral pathogens by protozoa. The expected outcomes are (i) the determination of the contribution of protists to human viral control in surface water and how this is affected by abiotic and biotic factors, (ii) an investigation of which virus species are affected and why the susceptibility to grazing is different among human viruses, (iii) an understanding of the underlying mechanisms of viral control by protists and (iv) a proposition of design, or improvement, of a water disinfection treatment based on grazing of human viruses by protists. This PhD will provide knowledge on how human viral pathogens are controlled by protists in aquatic ecosystems and how this could be used in man-made water treatment systems.