Cryptosporidium are parasitic protozoans that cause gastrointestinal disease and represent a significant risk to public health. Cryptosporidium oocysts are prevalent in surface waters as a result of human, livestock and native animal faecal contamination. The resistance of oocysts to the concentrations of chlorine and monochloramine used to disinfect potable water increases the risk of waterborne transmission via drinking water. In addition to being resistant to commonly used disinfectants, it is thought that oocysts can persist in the environment and be readily mobilized by precipitation events. This paper will review the critical processes involved in the inactivation or removal of oocysts in the terrestrial and aquatic environments and consider how these processes will respond in the context of climate change.