Every year in the United States cases of waterborne illness are generally characterized by gastrointestinal problems (vomiting, diarrhoea, etc.). However, these same symptoms can be more serious and even fatal in certain groups, such as the young, elderly, and those with compromised immune systems. Furthermore, viral pathogens found in groundwater are linked to chronic diseases such as adult onset diabetes and myocarditis. Recognizing that preventing contamination of water sources is the first step in the multiple barrier approach to drinking water protection, the Interim Enhanced Surface Water Treatment Rule (IESWTR) and the Disinfectants/Disinfection Byproducts Rule (DBPR) were released in 1999. The two rules will provide additional protection of public water supplies and address microbiological contamination. The rules address the risks of the trade-offs between disinfection necessary for microbial inactivation and the production of disinfection by-products. The requirements of 40 CFR 141.72(b) are consistent 99.99% removal and/or inactivation of viruses and 99% removal of Cryptosporidium oocysts. The code gives public water suppliers the option to demonstrate compliance through pilot plant studies or other means that combine filtration techniques with disinfection as in EPA 1999 Microbial and Disinfection Byproducts Rules Simultaneous Compliance Guidance Manual.

Presently, only surface water systems and systems using groundwater under the direct influence of surface water are required to disinfect their water supplies. Historically considered free of microbial contamination, most recent research has shown that aquifers can be readily contaminated by pathogens. To lessen the requirement for disinfection and to protect water resources, water suppliers have sought to use natural systems for Cryptosporidium oocysts removal. Thus, there is a critical need for information regarding the transport and fate of pathogens during water infiltration into subsurface systems.