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Members of these bacteria groups are most often used as indicators of possible sewage contamination because they are commonly found in human and animal feces. Although they are generally not harmful themselves, these bacteria may indicate the possible presence of other pathogenic (disease-causing) bacteria, viruses, and protozoans, such as dysentery, hepatitis A, and cholera (EPA 1986, 1997). As a result, their presence in streams is considered to pose a health risk. Sources of fecal contamination to surface waters include wastewater treatment plants, on-site septic systems, domestic and wild animal manure, and storm runoff. The bacteria groups have varying criteria levels. According to the California Department of Health, the maximum accepted level of coliform bacteria is 10,000 MPN/100 ml, based on a single water sample, for water contact recreation (DHS 2006). The EPA (1986) 7-day geometric mean E. coli criterion for water contact recreation, based on five or more samples per 30-day period, is 126 MPN/100 ml with a designated beach maximum of 235 MPN/100 ml. Enterococci concentrations in bathing beach waters should not exceed 61 MPN/100 ml (EPA 1986). Numerous water quality assessments report bacterial concentrations in exceedance of water quality criteria. Available data demonstrate elevated levels of bacteria concentrations within the lower Redwood Creek watershed (Stillwater 2005, Lendvay and Benning 2006, HI EA 2009). Amongst the studies, it is accepted that the primary sources of bacteria contamination include human septic sources, stable operations, restroom facilities and frequent human use. In the mid 1990s, the NPS implemented an intensive water quality monitoring program in the lower Redwood Creek watershed, focusing on stable operation and management practices at the Golden Gate Dairy (Vore 1997). During the 1997–1998 monitoring, waters were tested for fecal coliform at Muir Woods, Pacific Way, Muir Beach, Golden Gate Dairy, and Green Gulch Creek. In these tests, median fecal coliform at the upstream sites of Muir Woods and Green Gulch were within state criteria, while downstream samples at Pacific Way, Golden Gate Dairy, and Big Lagoon exceeded laboratory detection limits and exceeded health standards, indicating fecal coliform contamination (Stillwater 2005).

Lendvay and Benning (2006) reported 2006 fecal coliform measurements below the state maximum limit for fecal coliform of 400 colonies/100 ml. The highest bacterial count in the watershed was recorded at Muir Beach, the lowest elevational, and furthest downstream sampling site. As expected, Muir Beach also exhibited the highest number of E. Coli colonies (27 MPN/100mL ± 15.70), and highest enterococci count (117 MPN/100mL), both of which exceed state criteria limits (Lendvay and Benning 2006). Recent follow-up analysis of data collected by NPS in 2004–2005 conducted by Stillwater Sciences (2005) suggests current land use practices at the stables and other locations continue to result in excess nutrients and bacteria to the lower watershed. SWAMP monitoring conducted during the summer dry season, at a single location in Rodeo Creek reported E. coli concentrations of 120 MPN/100 ml (RWQCB 2009, 2010c). Sampling efforts reported in the Headlands Institute EA (2009) found Coliform counts in Rodeo Creek ranging between 240 and 900 fecal coliform units per 100mL; which exceeds surface water objectives. SWAMP monitoring in Tennessee Valley Creek did not include this parameter.

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