Water plays a major role in human disease by serving as the vehicle for the transmission of disease‐causing microorganisms (pathogens), and as a habit for some of their insect hosts. Worldwide, it is estimated that a child dies every 8 s from water‐related diseases. New pathogens, which are transmitted by water, are recognized on a continuing basis providing challenges to both watershed management and water treatment technologies. Microorganisms transmitted by the fecal‐oral route or waterborne pathogens are the most widespread since many may occur in the feces of both infected humans and animals. All surface waters can be expected to contain waterborne pathogens at one time or another. Feces from animals and sewage discharges contaminate surface waters. Groundwater may be contaminated from infiltration from land disposed human and animal wastes or water contaminated with these wastes, septic tanks, and unlined landfills. Contamination of surface and groundwater is always greatest after rainfall events due to the flushing of accumulated animal feces and infiltration of soils. Waterborne pathogens may survive for days to months in the environment. Survival of pathogens in the water environment is largely dependent on temperature and sunlight exposure.