It is essential that water be free of bacteria, viruses, and cysts. Pathogens in drinking water present immediate health risks and can be fatal. Every year thousands of cities are on boil water advisories due to the presence of pathogens in the public water systems.

Pathogenic microorganisms that occur in polluted water include protozoa, bacteria and enteric viruses. The most common disease this can cause is the gastrointestinal illness of diarrhea.  Although gastrointestinal illness is usually non-life threatening in normal healthy adults, the risk of death increases among vulnerable groups such as infants, the elderly and immunosuppressed individuals.

Coliform bacteria in drinking water is usually a result of a problem with the treatment system or the pipes which distribute water, and indicates that the water may be contaminated with germs that can cause disease.

Fecal Coliform and E coli are bacteria whose presence indicates that the water may be contaminated with human or animal wastes. Microbes in these wastes can cause short-term effects, such as diarrhea, cramps, nausea, headaches, or other symptoms. 

Turbidity can interfere with disinfection and provide a medium for microbial growth. It may indicate the presence of disease causing organisms. These organisms include bacteria, viruses, and parasites that can cause symptoms such as nausea, cramps, diarrhea, and associated headaches.

Cryptosporidium is a parasite that enters lakes and rivers through sewage and animal waste. It causes cryptosporidiosis, a mild gastrointestinal disease. However, the disease can be severe or fatal for people with severely weakened immune systems. EPA and CDC have prepared advice for those with severely compromised immune systems who are concerned about Cryptosporidium.