Protozoan parasites including Giardia, Cryptosporidium, and Entamoeba can be transmitted through water and cause disease in humans and animals. Control of waterborne infection can be accomplished through a variety of physical and chemical means, resulting in the production of safe drinking water and protection of public health. Coagulation and filtration are the most commonly employed methods for physical removal of parasites, while chlorine-based compounds, ozone, and ultraviolet light are used for inactivation. Combinations of treatment technologies can result in parasite removal/inactivation greater than 6-log, resulting in reliable public health protection.