The vast majority of bacteria in streams and lakes are ‘good’ bacteria.
They do not cause diseases and are necessary for healthy ecosystems to function
In almost all cases of water-borne illnesses the disease causing organisms, technically called pathogens or pathogenic organisms, come from untreated human waste or feces.
Direct testing for pathogens is expensive and impractical, as pathogens are rarely found because they usually occur sporadically and mostly at low levels. Instead, public health agencies look for the presence of “indicator” species, so called because their presence indicates that fecal contamination may have occurred. The two most commonly used indicators for recreational waters are fecal coliforms and E. coli (short for Escherichia coli). These are bacteria that live in the lower intestines of warm-blooded animals, including wildlife, farm animals, pets, and humans, and are excreted in their feces. In fact, the bacteria may constitute a significant fraction of fecal waste. E. coli and fecal coliform are not usually pathogenic, but their presence can indicate sewage contamination, perhaps accompanied by disease-causing pathogens.