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There are many kinds of waterborne parasites that might cause reactions. These include jellyfish blastocytes, which cause a condition known as "sea lice" and mature jellyfish. However, swimmer's itch usually refers to a reaction caused by trematode parasites, which can be found in fresh and salt water. These parasites are found in infected snails. In certain conditions – chiefly on warm, sunny days on calm, freshwater bodies such as lakes, but also in ocean water – the water warms to a temperature conducive for snails to grow and reproduce rapidly.

As this occurs, the snails release a type of larvae parasite known as cercariae into the water. These parasites find their way into the blood of aquatic and migrating birds (e.g., ducks, geese, gulls, swans) and mammals (e.g., muskrats and beavers), where the adult parasites live out their life cycle.

Once the birds and mammals become infected, the eggs of the parasite are passed into the water through the animals’ feces. The eggs contaminate the water when they hatch, releasing free-swimming larvae. The larvae search for a species of aquatic snail and infect the snail, and the life cycle begins over again. 

People who swim in this water may come into contact with the parasites. Soon after the parasites enter the superficial layers of human skin, they die, causing an allergic skin reaction known as swimmer itch.

The conditions that create swimmer itch are not always present. Once released into the water, larvae tend to live for about 24 hours without a host before dying. However, infected snails continue to produce the cercariae larvae throughout their lifetimes.

In some cases, exposure to algae, chemical pollutants or sewage may cause a form of dermatitis that is virtually indistinguishable from swimmer itch.