The quality of drinking water in the United States is among the best in the world; however, waterborne disease outbreaks continue to occur, and many more cases of endemic illness are estimated. Documented waterborne disease outbreaks are primarily the result of technological failures or failure to treat the water (Craun et al. 2006). Current federal regulations require that all surface waters used for a drinking water supply be treated to reduce the level of pathogens so as to reduce the risk of infection to 1:10,000 per year (Regli et al. 1991). To achieve this goal, water treatment must, at a minimum, reduce infectious viruses by 99.99% and protozoan parasites by 99.9% (Regli et al. 2003). If Cryptosporidium concentrations exceed a certain level in the source water, additional reductions are required. This degree of treatment is usually achieved by a combination of physical processes (coagulation, sedimentation, and filtration) and disinfection (chlorination, ozonation). Filtration is essential for the removal of protozoan parasites due to their resistance to chlorination and ozonation at doses normally used in drinking water treatment (Barbeau et al. 2000; Korich et al. 1990; Rennecker et al. 1999). A variance from filtration is allowed in some cases if the watershed is protected and carefully monitored for protozoan pathogens.