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Project: Fecal Indicator Bacteria (FIB) Levels during Dry Weather from Southern California Reference Streams

Background and Objectives

The presence of fecal indicator bacteria (FIB) in surface waters is a prevalent concern for many municipalities, health departments, and regulatory agencies. Persistent or excessive bacteria levels often result in reduced opportunities for beneficial uses such as swimming, and may lead to waterbodies being listed as impaired under Section 303(d) of the Clean Water Act. Management actions for impaired water bodies may include development of Total Maximum Daily Loads (TMDLs), issuance of National Pollutant Discharge Elimination System (NPDES) permits, and/or development of water quality plans that are intended to reduce bacteria levels to a point where water quality standards are met and beneficial uses are protected. An important step in the development of TMDLs and other water quality management plans is to identify all sources of the constituent(s) of concern in order to accurately quantify loads and set appropriate management or regulatory targets.

One of the challenges in developing these targets is accounting for an appropriate "natural" contribution of bacteria. Most watersheds consist of both developed and undeveloped areas, both of which can contribute bacteria to streams via surface runoff. Natural areas can be a source of bacteria originating from wildlife, including birds and mammals, pets, and livestock. Most previous studies of natural sources have focused on either short measurements during or immediately following storm water runoff, or on bacteria in coastal waters (beaches). Few studies have attempted to quantify naturally-occurring background levels of bacteria in streams during baseflow (i.e., non-storm) conditions over an extended period of time. Addressing this data gap is critical especially considering that streams and their associated coastal waters receive the most human use during the non-storm (i.e., summer) season.

The goal of this study was to establish a “reference” level of bacteria for use in setting appropriate water quality management targets. The study aimed to address the following questions:

a) What are the “background” ranges of concentrations of FIB associated with dry-weather runoff from natural areas?
b) What is the frequency with which reference FIB levels exceed relevant water quality standards?
c) How does seasonality influence stream FIB levels associated with reference areas?
d) How do the ranges of FIB concentrations associated with reference areas compare with those associated with urban (developed) areas?

Seasonal patterns in Enterococci levels at natural streams.


This project was completed in 2008.


To help establish a regional reference data set, bacteria levels were measured weekly at 15 unimpaired streams in 11 southern California watersheds weekly for one full year between March 2006 and March 2007. Water quality samples were analyzed for four bacteria indicators: E. coli, enterococci, total coliforms and Bacteroides thetaiotaomicron. In addition, weekly sampling included measures of flow and basic water quality parameters (e.g., temperature, pH, conductivity, dissolved oxygen).

Reference sites and the associated catchments sampled.

B. thetaiotaomicron are anaerobic bacteria that comprise the majority of microorganisms that inhabit the human digestive tract. As such, they may offer a more reliable measure of human fecal matter or pathogens than E. coli. The presence of B. thetaiotaomicron suggests that bacteria observed in the surface waters are predominantly of human origin. This analysis was initiated at a sampling site when the State of California single-sample water quality thresholds for both E. coli and enterococci were exceeded for two consecutive weeks. .

Data were analyzed to determine the frequency of exceedance of both the single sample and 30-day geometric mean freshwater bacteria standards. In addition, the data set was analyzed for temporal and spatial patterns to determine if bacteria levels varied as a function of location, stream type, or season.


This study yielded the following main conclusions:

• During dry weather conditions in natural streams, FIB typically occurred at levels below state water quality standards: annual mean concentrations (both single sample and 30-day geometric mean) were below established water quality criteria for all three regulated FIB indicators (E. coli, enterococci, and total coliforms). Only 18.2% of the indicator bacteria samples from the natural sites exceeded daily (single sample) water quality standards, where approximately 1.5%, 14%, and 3% of exceedences were due to E. coli, enterococci, and total coliforms, respectively.

• FIB in natural streams were most likely of non-human origin. All samples tested for the presence of B. thetaiotaomicron were negative, indicating contribution of only non-human sources in natural streams. FIB levels in natural streams likely result from a combination of natural inputs, such as wildlife, birds, and soil erosion and instream bacterial growth facilitated by high summer temperatures and presence of decaying organic matter.

• Dry weather FIB levels in natural streams were typically two orders of magnitude lower than those observed in streams draining developed watersheds. Data from the developed Ballona Creek watershed were typically in the 103 MPN/100 ml range for E. coli and enterococci. Even slight watershed modifications appeared to result in a relatively rapid departure from background FIB levels.

• FIB levels exhibited seasonal patterns. Mean bacteria levels and frequency of exceedance of water quality standards were higher during the warmer summer months for all three bacteria indicators. This suggests that summer is a critical period for assessing background bacteria levels.

• Bacteria levels in natural streams were generally higher during lower flow conditions. For all three indicators, densities increased exponentially when stream flow decreased below approximately 2 cubic feet/sec. In addition, median annual bacterial densities were higher in intermittent streams than in perennial streams, mainly during the period immediately prior to streams drying up.


This study was conducted in cooperation with a wide variety of partners including the City of San Diego, County of San Diego, Riverside County Flood Control District, San Bernardino County Flood Control District on behalf of the San Bernardino County Stormwater Program, Malibu Watershed TMDL workgroup, City of Laguna Niguel, Orange County Water District, Santa Ana Regional Water Quality Control Board, and San Diego Regional Water Quality Control Board.


LL Tiefenthaler, ED Stein, and GS Lyon. November 2008. Fecal Indicator Bacteria (FIB) Levels During Dry Weather for Southern California Reference Streams. Presented at Society of Environmental Toxicology and Chemistry (SETAC) 29th Annual Meeting.

For more information on Fecal Indicator Bacteria (FIB) Levels during Dry Weather from Southern California Reference Streams, contact Eric Stein at (714) 755-3233.
This page was last updated on: 7/2/2014