In 1998, an 8-mile reach of the Jacks Fork was included on Missouri's list of impaired waters as required by Section 303(d) of the Federal Clean Water Act. The identified pollutant on the Jacks Fork was fecal coliform bacteria. Potential sources of fecal contamination to the Jacks Fork include a wastewater treatment plant; campground pit-toilet or septic-system effluent; a large commercial, cross-country horseback trail riding facility; canoeists, boaters, and tubers; and cows.

The U.S. Geological Survey, in cooperation with the National Park Service, conducted a study to better understand the extent and sources of microbiological contamination within the Jacks Fork from Alley Spring to the mouth, which includes the 8-mile 303(d) reach. Identification of the sources would provide the National Park Service and the State of Missouri with the information needed to craft a solution of abatement, regulation, prevention, and mitigation with the end result being the removal of the Jacks Fork from the 303(d) list. Fifteen sites were sampled from November 1999 through December 2000. An additional site was sampled one time. Samples were collected mostly during base-flow conditions during a variety of nonrecreational and recreational season river uses. Samples were analyzed for selected fecal indicator bacteria, physical properties, nutrients, and wastewater organic compounds.

During the sampling period, the whole-body-contact recreation standard for fecal coliform (200 colonies per 100 milliliters of sample) was exceeded at three sites on August 10, 2000, and also at one site on May 11, June 7, and October 3, 2000. Fecal coliform densities and instantaneous loads generally increased from background concentrations at the Eminence site, peaked about 2 river miles downstream, and then decreased until the most downstream site sampled. Generally, the largest densities and loads at sites downstream from Eminence not related to wet-weather flow were observed during a trail ride held August 6 to 12, 2000.

A 24-hour sample collection effort was conducted the weekend of July 15 and 16, 2000, to investigate the effect that large numbers of swimmers, canoeists, and tubers had on fecal coliform densities in the Jacks Fork. Five or six samples were collected at six sites between Saturday morning and the following Sunday afternoon. No fecal coliform density at any of the sites sampled exceeded the whole-body-contact recreation standard.

Because bacteria survive longer in stream-bed sediments than in water, a source of bacteria in the water column could be from resuspension of accumulated bacteria from streambed sediments. Water and streambed-sediment samples were collected at three sites on August 3, 2000, 1 week before a trail ride and again at three sites on August 8, 2000, during a trail ride.

Sixty-five Escherichia coli isolates obtained from water samples collected at 9 sites and 23 Escherichia coli isolates obtained from stream-bed-sediment samples collected at 5 sites were submitted for ribotyping analysis. Samples were collected in 2000 during a variety of nonrecreational and recreational season river uses, including trail rides, canoeing, tubing, and swimming. Of the 65 isolates from water samples, 40 percent were identified as originating from sewage, 29 percent from horse, 11 percent from cow, and 20 percent from an unknown source. Of the 23 isolates from streambed-sediment samples, 39 percent were identified as originating from sewage, 35 percent from horse, 13 percent from cow, and 13 percent from unknown sources.

Analysis of physical property (dissolved oxygen, pH, specific conductance, and temperature) and nutrient (dissolved nitrite plus nitrate and total phosphorus) data indicated that overall few statistically significant differences occurred among the main stem sites of the Jacks Fork. A significant increase in total phosphorus concentrations did occur at site 75 immediately downstream from the Eminence Wastewater Treatment Plant, but the effect diminished quickly downstream. Unlike fecal coliform bacteria, most variations in physical property values or nutrient concentrations were related to seasonal changes, time of day the sample was collected, or hydrologic conditions and not to certain recreational activities.

Trace quantities of wastewater organic compounds were detected in all waters sampled for these constituents. Two of the compounds were detected in associated laboratory blanks, and other detected compounds have sources other than sewage effluent. The best indicators of municipal or domestic sewage effluent were the non-ionic detergent metabolites (nonylphenol monoethoxylate, octylphenol monoethoxylate, and para-nonylphenol), phenol, and caffeine; but possible sources of these compounds, which were detected in one or more of the samples, could be the numerous campers, swimmers, and canoeists that were present when the samples were collected.