Cryptosporidium causes cryptosporidiosis, an infection that may present as a diarrhoeal with or without a persistent cough in immune competent hosts. Other apicomplexan pathogens include the malaria parasite Plasmodium and the toxoplasmosis parasite Toxoplasma. Unlike Plasmodium, which transmits via a mosquito vector, Cryptosporidium does not use an insect vector, and is capable of completing its lifecycle within a single host, resulting in cyst stages that are excreted in feces or through inhalation of coughed on fomites and are capable of transmission to a new host

Many treatment plants that take raw water from rivers, lakes, and reservoirs for public drinking water production use conventional filtration technologies. Direct filtration, which is typically used to treat water with low particulate levels, includes coagulation and filtration but not sedimentation. Other common filtration processes including slow sand filters, diatomaceous earth filters, and membranes will remove 99% of Cryptosporidium. Membranes and bag- and cartridge-filter products remove Cryptosporidium specifically.

Cryptosporidium is highly resistant to chlorine disinfection; but with high enough concentrations and contact time, Cryptosporidium inactivation will occur with chlorine dioxide and ozone treatment. In general, the required levels of chlorine preclude the use of chlorine disinfection as a reliable method to control Cryptosporidium in drinking water. Ultraviolet light treatment at relatively low doses will inactivate Cryptosporidium. Calgon Carbon-funded research originally discovered UV's efficacy in inactivating Cryptosporidium.

One of the largest challenges in identifying outbreaks is the ability to verify the results in a laboratory. The oocytes may be seen by microscopic examination of a stool sample, but they may be confused with other objects or artifacts similar in appearance. Most cryptosporidia are 3–6 μm in size, although some reports have described larger cells. Boiling is believed to be the safest option for water contaminated by Cryptosporidium.

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