Source: Martin CathraeAnimal waste is often used as a natural fertilizer in agriculture; however, if not properly managed or treated it can be one of the main sources of microbial contaminants in a water supply, which has the potential to causing disease. Animal waste can threaten source water when domesticated animals have access to rivers allowing them to defecate in the water, or where confined animal facilities directly runoff into streams or rivers. Manure can also contaminate groundwater where the liquid waste from factory farms is drained into boreholes.

Common types of microbial contamination include:

• Campylobacter: This type of bacteria causes inflammation of the stomach and intestines and causes diarrhea. It is found in contaminated human and animal wastes. Symptoms begin 2 to 5 days after exposure and continue for about 1 week.
• Escherichia coli: This bacterium is naturally present in human and animal intestines and plays an important role in the process of digestion. However, some forms of E. coli can cause severe forms of diarrhea that can lead to kidney failure and death. Untreated sewage is a common source of E. coli contamination.
• Giardia: A type of parasite often found in water which can cause giardiasis or "beaver fever" that infects the gastrointestinal tract. Symptoms of giardia may include diarrhea, nausea, and cramps and vomiting, however symptoms can appear between 7 to 10 days after exposure. Wilderness campers and others who drink untreated surface water are most susceptible to giardia exposure
• Cryptosporidium: a type of parasite which can cause the disease cryptosporidiosis. It is contracted by drinking water that has been in contact with waste from an infected human or animal. It affects the intestines, and can cause diarrhea, stomach cramps or a low fever, with symptoms appearing between 2 and 10 days after exposure. For people with a weak immune system, cryptosporidiosis can be fatal.

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Adapted from Pollution Probe's Source Water Protection Primer and Drinking Water Primer; Health Canada's Giardia And Cryptosporidium In Drinking Water Fact Sheet; and the USDA's Foodborne Illnesses: Campylobacter Questions and Answers