U.S. Department of the Interior

U.S. Geological Survey

Fact Sheet 2011–3095

January 2012

Evaluation of Fecal Contamination by Human and Ruminant 

Sources in Upper Fountain Creek, Colorado, 2007–2008, 

By Using Multiple Lines of Evidence

Printed on recycled paper

In May 2007, the U.S. Geological 

Survey, in cooperation with the Pikes 

Peak Area Council of Governments, 

Colorado Department of Public Health 

and the Environment, Colorado Springs 

Engineering, and Colorado Springs 

Utilities, began a study to document the 

locations, magnitude, and sources of fecal 

contamination to upper Fountain Creek, 

Colorado (fig. 1). Upper Fountain Creek 

extends from the headwaters, near Green 

Mountain Falls, Colorado, to the confluence of Monument Creek with Fountain 

Creek in Colorado Springs, Colorado. 

Measured densities of Escherichia 

coli (E. coli) in Fountain Creek were 

more than 126 per 100 milliliters (the 

Colorado criterion for recreational uses; 

Colorado Department of Public Health 

and Environment, 2005) at several sites 

in the study area. Exceedances occurred 

during warm-weather months (warm 

season, June 15 through September 15) 

in Ruxton Creek (site 9), Fountain Creek 

downstream from Ruxton Creek (site 10), 

and Fountain Creek below 8th Street in 

Colorado Springs (site 15).

Samples collected in the study 

area generally met the E. coli criterion 

throughout the cool-weather months (cool 

season, September 16 through June 14) 

and during the warm season in Fountain 

Creek upstream from Ruxton Creek. 

Data indicated that human sources rarely 

accounted for most E. coli observed during exceedances; rather, data indicated 

that other sources, particularly birds, likely 

were the dominant source of E. coli during 

exceedances of the standard.

Study Objectives

In 2008, Fountain Creek was placed 

on the Colorado 303(d) list of impaired 

streams because of fecal contamination 

(Colorado Department of Public Health 

and Environment, 2008). The objective of 

this study was to identify major sources 

of E. coli in upper Fountain Creek during 

Fountain Creek is a high-gradient stream on the Front Range of the Rocky 

Mountains in Colorado (fig. 1). The headwaters of Fountain Creek drain Pikes 

Peak, a major destination for tourism. Fountain Creek is a drinking-water source 

for the City of Colorado Springs, Colorado, and is used for irrigation, recreation, 

and other purposes between Colorado Springs and the confluence with the 

Arkansas River at Pueblo, Colorado. In 2008, Fountain Creek was placed on the 

Colorado 303(d) list of impaired streams because of fecal contamination. Colorado 

uses a 30-day geometric mean standard of 126 E. coli per 100 milliliters as its 

management goal for recreational waters (Colorado Department of Public Health 

and Environment, 2005). 

Upper Fountain Creek is mostly undeveloped except for substantial populations around Manitou Springs and Colorado Springs. Likely controllable sources 

of fecal contamination , identified by local water managers, include humans, 

horses, grazing cattle, wildlife, and domestic pets. E. coli sampling began at 

16 sites during the first year of the study. Based on these data, areas where E. coli 

tended to exceed the State’s recreational water standard were selected to track 

fecal contamination in more depth during the second year of the study: 

• Upstream from Manitou Springs (site 2: Fountain Creek below Green Mountain 

Falls), 

• Within Manitou Springs (sites 7.9, 9, and 10: Fountain Creek above Ruxton Creek, 

Ruxton Creek at mouth, and Fountain Creek below Ruxton Creek, respectively),

• Between Manitou Springs and Colorado Springs (site 15: Fountain Creek below 

8th Street) 

Fountain Creek






The Clean Water Act of 1972 requires that all waters of the United States be classified according to designated uses 

(U.S. Environmental Protection Agency, 2010). Each state has its own system of designated uses: examples of these designated 

uses include habitat for fish and wildlife, industrial uses such as cooling water, and recreation. The major limitation for recreational uses is public health risk caused by fecal contamination. Although the U.S. Environmental Protection Agency (USEPA) 

currently (2010) is re-evaluating the way that public health risk is measured, the criteria in effect at the time of this research 

require measurement of Escherichia coli (E. coli) or enterococci, another type of fecal-indicator bacteria.

USEPA puts forth guidance for the states so that each state may regulate its water to meet designated uses. The most-recent 

criteria that USEPA put forward were in 2004, in support of the BEACH Act of 2000 that covers recreational water quality at 

coastal and Great Lakes’ beaches. These criteria are essentially the same as those put forth in 1986 for swimming beaches and 

non-swimming recreational uses. The USEPA criteria are published as part of the Code of Federal Regulations and are available 

at http://www.epa.gov/beaches/.

Although many states have no coastal or Great Lakes beaches, the criteria published by USEPA commonly are applied to 

inland recreational waters. The State of Colorado created its recreation water standards based generally on the USEPA criteria. 

The Colorado standard specifies that Class E (existing) recreational waters must maintain a geometric mean concentration of 

E. coli that is less than 126 per 100 milliliters. In Colorado and other States, the Clean Water Act of 1972 requires adding waterways that do not meet standards for their designated use to a list of “impaired” waterways. Under the Clean Water Act of 1972, 

existing management of impaired waterways is insufficient to bring E. coli to within standards, a Total Maximum Daily Load 

(TMDL) plan must be created to manage E. coli contamination in that waterway.

Figure 1. Locations of sampling sites in the Fountain Creek and Ruxton Creek watersheds, 

Colorado, 2007 to 2008. Various municipalities are shown as shaded areas. Sample sites 

are indicated with numerals (1 to 15). Numerals that are bold underlined indicate intensivemonitoring sites at which a full suite of analytes was evaluated.

exceedances of the State recreational water 

standard. To meet this objective, a new 

approach was developed and tested that 

uses genetic marker analysis for microbial source tracking (MST, see sidebar 

for definition), along with other information, to evaluate potential contributions of 

fecal contamination from various sources 

(Stoeckel and others, 2011). Knowledge of 

sources will allow water-quality managers 

to make decisions based on health risks 

associated with feces from those sources.

Evaluation of Fecal Contamination 

by Human and Ruminant Sources

The initial E. coli survey at 16 sites in 

2007 (Stoeckel and others, 2011), identified the location where Ruxton Creek 

enters Fountain Creek as a pivotal point 

in the watershed (sites 7.9, 9, and 10). 

At this location, Fountain Creek often 

changed from achieving to failing to 

achieve Colorado’s standard for in-stream 

E. coli density. Ruxton Creek accounted 

for some, but not all, of the fecal contamination at this point. In addition to this 

location, Fountain Creek below Green 

Mountain Falls (site 2) had occasional 

exceedances of the Colorado standard, and 

Fountain Creek below 8th Street (site 15; 

the downstream-most site) consistently 

Microbial Source Tracking of Fecal Contamination: Why E. coli?

USGS gage

North Pole

Garden of the Gods

Pikes Peak

Cave of the Winds

Manitou Cliff Dwellings

Cascade

Colorado Springs

Manitou Springs

Green Mountain Falls

15

8

10 11 9

7

6

5

4

3

1

14

13

12

2

7.9

EL PASO COUNTY

TELLER

COUNTY

Ruxton Creek

Monum ent Creek

FountainC reek

EXPLANATION

Point of Interest

Ruxton Creek Sample Site

Fountain Creek Sample Site

Manitou and Pikes Peak Cog Railroad

Watershed Boundary

Cascade

Colorado Springs

Green Mountain Falls

Manitou Springs

Pueblo

Denver

Woodland Park Colorado

Springs

COLORADO

0 1 2 3 4 KILOMETERS

0 1 2 3 4 MILES
exceeded the E. coli standard during the 

warm season. In both years of sampling, 

E. coli densities generally were higher during the warm season than during the cool 

season (figs. 2 and 3).

Water was tested for total fecal contamination and contamination from human 

and ruminant sources by use of MST 

genetic marker tests. If humans or ruminants (cattle, deer, elk, and sheep) were 

the source of high concentrations of E. coli

during the warm season, the genetic markers for those animals would increase in the 

warm season. However, the various MST 

genetic markers did not increase during 

the warm season (fig. 3).

During the cool season, MST marker 

analysis did not exclude any of the evaluated animals (human, ruminant, pet, bird, 

other nonruminants) as potential sources 

of fecal contamination. However, because 

the levels of E. coli generally were below 

the standard during these months, the 

presence of fecal contamination from any 

of these sources did not exceed regulations. However, during warm season, MST 

marker analysis indicated that humans, 

ruminants, and pets (cats and dogs) could 

not have been the source of excessive 

E. coli (relative to the standard).

Birds were the only evaluated source 

that could have contributed this much 

E. coli without being detected by MST 

genetic markers. In the area of Manitou 

Springs, pigeons were observed roosting in large numbers under bridges and 

buildings near Fountain Creek. In the area 

between Manitou Springs and Colorado 

Springs, other birds may be a more likely 

explanation than pigeons.

Water also was tested for wastewaterassociated chemicals. If human sources 

of fecal contamination caused increased 

E. coli density then wastewater-associated 

chemicals might be present. Although 

these chemicals were detected more often 

in developed areas of Manitou Springs and 

Colorado Springs, they were not detected 

more often during the warm season 

(high E. coli) than during the cool season 

(low E. coli). Many samples with high 

E. coli concentrations had no detectable 

wastewater chemicals, implying absence 

or low concentration of human-source 

fecal contamination.

Figure 2. E. coli density measurements during the year-long 

intensive monitoring, August 2007 through September 2008. 

For the purposes of this plot, warm season extended from 

June 15 through September 15, and cool season extended from 

September 16 through June 14. Warm season and cool season 

values are associated with the same sites, but are offset from 

the true site identifier to enhance visual clarity.

Figure 3. Example microbial source tracking marker 

concentration measurements (human-associated marker qHF183) 

during the year-long intensive monitoring, August 2007 through 

September 2008. For the purposes of this plot, warm season 

extended from June 15 through September 15, and cool season 

extended from September 16 through June 14. Warm season and 

cool season values are associated with the same sites, but are 

offset from the true site identifier to enhance visual clarity.

1 2 3 4 5 6 7 9 10 11 12 13 14 15

Site identifier

7.9

2

3

4

5

6

7

Log(adjusted qHF183 concentration)

(copy/100 millimeters)

Cool season, Fountain Creek

Warm season, Fountain Creek

Cool season, Ruxton Creek

Warm season, Ruxton Creek

EXPLANATION

1 2 3 4 5 6 7 9 10 11 12 13 14 15

Site identifier

7.9

1

10

100

1,000

10,000

100,000

E. coli density 

(most probable number per 100 millimeters)

Cool season, Fountain Creek

Warm season, Fountain Creek

Cool season, Ruxton Creek

Warm season, Ruxton Creek

Colorado Standard

EXPLANATION
Conclusions

The general lack of wastewaterassociated chemicals in the water 

samples during the warm season supported the finding that humans or ruminants were not the primary cause of fecal 

contamination to upper Fountain Creek. 

This lack of wastewater-associated 

chemicals was not an artifact of analysis; in five samples (20 percent of the 

samples with high concentrations of 

E. coli), high levels of E. coli coincided 

with detection of human-associated 

genetic marker, elevated ammonia 

concentrations and above-backgroundlevel detections of wastewaterassociated chemicals.

The indication that birds were a 

probable source of E. coli contamination 

during warm season was supported by the 

data collected. In water samples collected 

during the warm season and in bird-feces 

samples, high concentrations of E. coli

were present but the general-feces MST 

marker concentration was low relative to 

other potential fecal sources and humanand ruminant-associated markers were 

absent. Furthermore, the absence of 

human-associated wastewater compounds 

in these water samples was consistent 

with bird sources. Bird droppings were 

the only source of E. coli that was evaluated that had characteristics consistent 

with the water data collected.

Human, ruminant, and pet sources 

would not have been excluded as probable dominant sources of fecal contamination to upper Fountain Creek except 

through application of the new methods 

developed for this study. The validation of this approach was supported 

with additional lines of evidence. The 

use of microbial source tracking to help 

understand E. coli contamination led to 

unexpected findings in upper Fountain 

Creek. The same approach could result 

in useful information in other areas of 

Colorado, and in other States, where 

recreational-water quality standards are 

exceeded and the sources of contamination are unknown.

Contact information

David Mau

Southeast Colorado Hydrologic Studies Chief

USGS Colorado Water Science Center

Phone: 719-544-7155

dpmau@usgs.gov

Donald Stoeckel

PhD, Principal Investigator

Phone: 614-670-9302

don@dsH2O.com

For more information, contact

Southeast Colorado Chief, USGS Colorado Water Science Center

201 East 9th Street

Pueblo, CO 81003

Phone: (719) 544-7155

Or visit the Colorado Water Science Center Web site at http://co.water.usgs.gov/

This publication is available online at URL http://pubs.usgs.gov/fs/2011/3095/

References Cited

Colorado Department of Public Health and 

the Environment, 2005, Section 303(d) 

list water-quality-limited segments 

requiring TMDLs (5 CCR 1002-93): 

Water Control Commission, regulation 

no. 93.

Colorado Department of Public Health 

and the Environment, 2008, The basic 

standards and methodologies for surface 

water (5 CCR 1002-31): Water Control 

Commission, regulation no. 31.

Stoeckel, D.M., Stelzer, E.A., Stogner, 

R.W., and Mau, D.P., 2011, Semiquantitative evaluation of fecal contamination potential by human and ruminant 

sources using multiple lines of evidence: 

Water Research, v. 45, p. 3225–3244.

U.S. Environmental Protection Agency, 

2010, National summary of impaired 

waters and TMDL information: Accessed 

April 15, 2011, at http://iaspub.epa.gov/

waters10/attains_nation_cy.control?p_

report_type=T.

—Donald Stoeckel