Parasites include several thousand types of organisms with many that result in waterborne illness such as giardia and cryptosporidium. Sometimes there are harmful viruses, bacteria and parasites in the water that can cause ear and eye infections, gastrointestinal illness, or skin disease and irritation. Viruses, bacteria, and parasites can enter waterbodies through a variety of routes including runoff from agricultural and urban areas into surface waters and through leaching into groundwater. Essentially all areas of the coastal environment have the potential for contamination by microbial pathogens. Bacteria, viruses and parasites can be a health concern in freshwater ponds and rivers, brackish estuaries and sounds, and in the open ocean, especially those areas close to stormwater and wastewater treatment plant outfalls.
Microbial pathogens can also be a risk in poorly chlorinated swimming pools.
State public health officials began testing coastal recreation waters in the summer of 1997 to make sure they are safe for swimming. If a certain area along the coast is identified as having a problem with water quality, health officials recommend people not swim there by posting a sign in the area, listing it on their web site, and by notifying the local media and the county health department. The state tests for the presence of fecal coliform bacteria, which are not harmful bacteria but rather an indicator of the presence of waste from warm-blooded animals. Waste from warm-blooded animals, including humans, can contain harmful bacteria, viruses, or parasites. When the average coliform count over a five-week period exceeds more than 200 per hundred milliliters of water, the area is placed under an advisory for recreational activity because it is considered to have a higher risk of causing illness.