The following is from the U.S. EPA website on water quality monitoring

5.11 Fecal Bacteria

What are fecal bacteria and why are they important?

Members of two bacteria groups, coliforms and fecal streptococci, are used as indicators of possible sewage contamination because they are commonly found in human and animal feces. Although they are generally not harmful themselves, they indicate the possible presence of pathogenic (disease-causing) bacteria, viruses, and protozoans that also live in human and animal digestive systems. Therefore, their presence in streams suggests that pathogenic microorganisms might also be present and that swimming and eating shellfish might be a health risk. Since it is difficult, time-consuming, and expensive to test directly for the presence of a large variety of pathogens, water is usually tested for coliforms and fecal streptococci instead. Sources of fecal contamination to surface waters include wastewater treatment plants, on-site septic systems, domestic and wild animal manure, and storm runoff.

In addition to the possible health risk associated with the presence of elevated levels of fecal bacteria, they can also cause cloudy water, unpleasant odors, and an increased oxygen demand. (Refer to the section on dissolved oxygen.)

Indicator bacteria types and what they can tell you

The most commonly tested fecal bacteria indicators are total coliforms, fecal coliforms, Escherichia coli, fecal streptococci, and enterococci. All but E. coli are composed of a number of species of bacteria that share common characteristics such as shape, habitat, or behavior; E. coli is a single species in the fecal coliform group.

Total coliforms are a group of bacteria that are widespread in nature. All members of the total coliform group can occur in human feces, but some can also be present in animal manure, soil, and submerged wood and in other places outside the human body. Thus, the usefulness of total coliforms as an indicator of fecal contamination depends on the extent to which the bacteria species found are fecal and human in origin. For recreational waters, total coliforms are no longer recommended as an indicator. For drinking water, total coliforms are still the standard test because their presence indicates contamination of a water supply by an outside source.

Fecal coliforms, a subset of total coliform bacteria, are more fecal-specific in origin. However, even this group contains a genus, Klebsiella, with species that are not necessarily fecal in origin. Klebsiella are commonly associated with textile and pulp and paper mill wastes. Therefore, if these sources discharge to your stream, you might wish to consider monitoring more fecal and human-specific bacteria. For recreational waters, this group was the primary bacteria indicator until relatively recently, when EPA began recommending E. coli and enterococci as better indicators of health risk from water contact. Fecal coliforms are still being used in many states as the indicator bacteria.

E. coli is a species of fecal coliform bacteria that is specific to fecal material from humans and other warm-blooded animals. EPA recommends E. coli as the best indicator of health risk from water contact in recreational waters; some states have changed their water quality standards and are monitoring accordingly.

Fecal streptococci generally occur in the digestive systems of humans and other warm-blooded animals. In the past, fecal streptococci were monitored together with fecal coliforms and a ratio of fecal coliforms to streptococci was calculated. This ratio was used to determine whether the contamination was of human or nonhuman origin. However, this is no longer recommended as a reliable test.

Enterococci are a subgroup within the fecal streptococcus group. Enterococci are distinguished by their ability to survive in salt water, and in this respect they more closely mimic many pathogens than do the other indicators. Enterococci are typically more human-specific than the larger fecal streptococcus group. EPA recommends enterococci as the best indicator of health risk in salt water used for recreation and as a useful indicator in fresh water as well.

Which Bacteria Should You Monitor?

Which bacteria you test for depends on what you want to know. Do you want to know whether swimming in your stream poses a health risk? Do you want to know whether your stream is meeting state water quality standards?

Studies conducted by EPA to determine the correlation between different bacterial indicators and the occurrence of digestive system illness at swimming beaches suggest that the best indicators of health risk from recreational water contact in fresh water are E. coli and enterococci. For salt water, enterococci are the best. Interestingly, fecal coliforms as a group were determined to be a poor indicator of the risk of digestive system illness. However, many states continue to use fecal coliforms as their primary health risk indicator.

If your state is still using total or fecal coliforms as the indicator bacteria and you want to know whether the water meets state water quality standards, you should monitor fecal coliforms. However, if you want to know the health risk from recreational water contact, the results of EPA studies suggest that you should consider switching to the E. coli or enterococci method for testing fresh water. In any case, it is best to consult with the water quality division of your state's environmental agency, especially if you expect them to use your data.

The first two rows in the table below give the acceptable standards for bacteria levels in a waterbody. All streams in this study area are classified as Class B Warmwater Fisheries (BWWF).

As you can see by the tables below these standards are not being met.