Both agriculture and sewage treatment produce inputs into rivers with very high concentrations of bacteria and viruses including a wide range of pathogenic organisms. Even in areas with little human activity significant levels of bacteria and viruses can be detected originating from fish and aquatic mammals and from animals grazing near rivers such as deer. Upland waters draining areas frequented by sheep, goats or deer may also harbour a variety of opportunistic human parasites such as liver fluke. Consequently, there are very few rivers from which the water is safe to drink without some form of sterilisation or disinfection. In rivers used for contact recreation such as swimming, safe levels of bacteria and viruses can be established based on risk assessment.
Under certain conditions bacteria can colonise freshwaters occasionally making large rafts of filamentous mats known as sewage fungus – usually Sphaerotilus natans. The presence of such organisms is almost always an indicator of extreme organic pollution and would be expected to be matched with low dissolved oxygen concentrations and high BOD values.
E. coli bacteria have been commonly found in recreational waters and their presence is used to indicate the presence of recent fecal contamination, but E. coli presence may not be indicative of human waste. E. coli are found in all warm-blooded animals. E. coli have also been found in fish and turtles. Enterobacteria may also persist in the environment in mud, sediments, sand and soil for considerable lengths of time.