Bacteria
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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.

Stream Team collects samples that are brought back to the Channelkeeper lab and analyzed for three types of bacteria:

Total Coliform: Total coliforms are a widespread group of bacteria in nature. All members of the total coliform group can occur in human feces, but some can also be present in animal manure, soil, vegetation 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 found are fecal and human. For recreational waters, total coliforms are no longer recommended as an indicator, but they are still the standard test for drinking water because their presence indicates contamination of a water supply by an outside source.

E. Coli: 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.

Enterococcus: Enterococci are a subgroup of the fecal streptococci bacteria, and are typically more human-specific. Enterococci are distinguished by their ability to survive in salt water, and in this respect they more closely mimic many pathogens than the other indicators. The 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.

Bacteria are reported as the "most probable number" (MPN) of bacteria in 100 milliliters (100 ml, about 4 ounces) of water; we use a statistical test instead of directly counting bacteria so the actual number is an estimate. California Public Health requirements for bacteria counts are complicated and vary somewhat by jurisdiction; what follows is simply a broad outline. There are two limits for each test, a single sample limit and a limit for an average of 5 or more weekly samples. For recreational use, the total coliform limits are "no more than 10,000 per 100 ml in a single sample, and an average of less than 1000." For E. coli the "average" limit is 126 bacteria/100 ml of water and the single sample limit varies from 235 to 500 depending on intensity of use (235 for beach areas, 500 for occasional use). For enterococcus the "average of 5 or more samples" limit is 35 and the single sample limit is 104 (there is general agreement on the 35 limit, but various jurisdictions in the state vary the single sample limit between 104 and 500).

Observations made on Stream Team about bacterial levels: