From swimming pools to wells, chlorine is a common chemical used to disinfect water sources.
Helicobacter pylori is known to cause gastritis and peptic ulcers.
Studies done in Peru (citation needed) and Japan (citation needed) have shown the presence of the bacteria in public water sources, proving its possibility as a waterborne microbe.
Cryptosporidium parvum is a type of parasite capable of causing gastrointestinal illness. Unlike Helicobacter pylori, however, Cryptosporidium has been proven to be unresponsive to chlorination (citation needed).
Scientists are not content with shock chlorination. As technology advances, methods to improve both testing and disinfection are created.
Hulten K., Han S.W., Enroth H., Klein P.D., Opekun A.R., Gilman R.H., Evans D.G., Graham D.Y., El-Zaatari F.A. "Helicobacter pylori in the drinking water in Peru. Gastroenterology. April 1996. Volume 110(4). p. 1031-5.