This article is part of a larger series that investigates what we know about local tributaries around Lake Pepin. Follow us online and sign-up for our e-newsletter so you don’t miss the next release. If you have information or pictures for other Lake Pepin tributaries, please email us at: info@lakepepinlegacyalliance.org.

Mississippi River-Lake Pepin (MRLP) watershed and tributaries (Minnesota Pollution Control Agency, 2012)

By: Emily Green

Miller Creek is one of several small tributaries flowing into Lake Pepin out of the Mississippi River-Lake Pepin (MRLP) watershed. Originating about five miles southwest of Lake City in northern Wabasha County, it meanders northeast for several miles then turns east near County Hwy 9, entering Lake Pepin about a half mile south of Lake City. Its 11,000+-acre watershed includes an upland landscape of gently rolling croplands and pastures and a downstream landscape that drops steeply through forested valleys and grasslands. Like several other MRLP tributaries, Miller Creek is a designated cold-water trout stream. Also like others, in 2012 it was listed as impaired by fecal coliform bacteria, specifically E. coli.

Unfortunately, elevated bacteria levels are not uncommon in SE Minnesota waters. In 1998, 20 southeastern MN streams were listed as impaired by fecal coliform bacteria. As per U.S. EPA requirements, The Minnesota Pollution Control Agency (MPCA) worked with local partners to develop a 2003 Total Maximum Daily Load (TMDL) study for that group of water bodies. Another TMDL was created in for the Mississippi River-Lake Pepin Tributaries in 2013. TMDLs determine the level of a pollutant that a water body can accept and still meet water quality standards, and the report includes strategies to reduce the pollutant.

E. coli occurs naturally in the gastrointestinal tracts of warm-blooded creatures, ergo in human and animal waste. Most of its strains are not harmful to humans, but a few can cause intestinal illness when ingested. Elevated E. coli levels in water warrant concern because of the potential presence of those harmful strains, but more importantly because E. coli has long been considered an indicator of animal or human fecal contamination, which could contain even more dangerous microbial bacteria associated with feces. E. coli is a key “fecal indicator organism” in large part because it can be relatively easily and inexpensively measured.

Miller Creek flowing into Lake Pepin (LPLA, 2020)

Fecal bacterial contaminants can enter surface waters in a variety of ways, including nonpoint sources such as animal feedlot runoff, erosion from manure-treated fields, leaky septic systems, or a point source such as a municipal wastewater treatment facility. Depending on how bacteria enter a given water body, there are an array of strategies known to help stem the contaminant flow including fixing feedlot runoff issues, helping landowners fine-tune the timing of manure applications or limit erosion, adding fencing, promoting rotational grazing, expanding conservation tillage, fixing leaky septics, and improving residential wastewater treatment systems.

DNA testing to determine whether a given site’s bacteria population is human or animal can help clarify which of the remediation strategies should be prioritized to reduce that site’s pollutant loading. In Miller Creek’s case, DNA fingerprinting was done in 2013 and the results were inconclusive, which, according to Goodhue County SWCD Water Planner Beau Kennedy, was a “real head scratcher.”

Kennedy explained that it’s challenging to understand the high E. coli levels in Miller Creek—some readings nearly 10 times greater than the acceptable level--as the watershed has relatively low concentrations of both animal units and septic systems, and no point sources. Moreover, he said it has been frustrating that over two rounds of water quality testing—in 2012-13 and in 2018-2019—they have seen no change in bacteria levels despite ongoing implementation of BMPs. Kennedy stressed that despite the continued high numbers he’s not aware of any human or animal illness to date in connection with Miller Creek’s waters.

(Site specific surface water monitoring data can be accessed from the MPCA here.)

According to MPCA SE Watershed Unit Supervisor Justin Watkins, the fact that we don’t fully understand the bacterial contamination picture at Miller Creek is “not a big surprise when you consider we are talking about living organisms in natural systems. We don’t have a ‘perfect’ indicator of harmful pathogens. We use E. coli because it’s currently the best indicator available to us.”

In fact, research findings since the mid-2000s have begun challenging and expanding long-standing beliefs about the nature of E. coli, and its use as a fecal indicator. Scientists long believed that E. coli could survive for only a limited time outside of animal GI tracts. Thus, its presence in surface waters was thought to definitively indicate recent or ongoing fecal contamination. However, recent research indicates that in fact some E. coli can persist in certain soil and sediment conditions, and some E. coli may become naturalized to certain sites and persist over a long term (Ishii et al. 2006, Ishii and Sadowsky 2008, Chandrasekaran et al. 2011). A study by Luo et al. (2011) suggests that naturalized E. coli could be widespread in nature, may be truly environmentally adapted--i.e., not associated with a mammalian host--and therefore unlikely to be useful as a fecal contamination indicator.

According to Kennedy, this phenomenon of E. coli persisting in sediment “could play a role” in the high levels and perplexing findings at Miller Creek. Additional DNA testing might help clarify the picture, however it is very expensive. “We don’t have an explicit plan to do more DNA testing but we are not ruling it out. We know that we need to continue to study this issue and we are always looking to improve our understanding,” stated Watkins.

Yet even without knowing the source of Miller Creek’s E. coli, natural resource professionals in Wabasha and Goodhue county SWCDs have been working hard and will continue to prioritize helping landowners implement the best management practices that are known to help reduce waterborne pathogen levels. Watkins stressed that “despite the complex nature of pathogens in the natural environment, we do have great confidence that managing obvious, clear pollution hazards like failing septics and feedlot runoff is having positive impacts in southeast Minnesota.” He added, “Southeast Minnesota has done a great job of addressing both [human and animal] sources. There’s still more work to do but a lot of good already out there on the ground.”

(The Watershed Restoration and Protection Strategy Report for the Lake Pepin-Mississippi River was published in 2015.)

While it’s possible that new research and data could lead to reevaluating Miller Creek’s bacterial contamination situation in future, for the moment it’s clear that people should continue to exercise care around Miller Creek and any waters with established elevated contaminant levels and wash thoroughly if they come into contact with the water. MPCA guidance on avoiding waterborne pathogens advises: “Use common sense to reduce your risk of pathogen exposure. Pathogens are more likely present if stream levels are high or the water is muddy. Consider delaying your water recreational activity until conditions improve.”

Miller Creek streambank erosion (MN DNR)

Fortuitously, some of the good work being done to control pathogen runoff is broadly helpful for reducing soil erosion and sedimentation that could be carried downstream into Lake Pepin. While Miller Creek and the other MRLP tributaries do not generally have excessive sediment and are not major contributors to Lake Pepin’s sediment problems (contributing only an estimated 2% of Lake Pepin’s sediment load), reducing soil erosion and improving upstream water storage are widely agreed upon as valuable and important goals with multiple benefits to the landscape and local water bodies.

In 2015, a $317,000 Minnesota’s Clean Water Fund (CWF) grant and a $146,000 EPA grant were awarded to Goodhue County SWCD, working in partnership with Wabasha SWCD, to fund an array of work aimed at improving water storage and reducing erosion throughout the MRLP watershed. With that funding, 44 earthen dams, designed to hold water temporarily and release it slowly, were built across the watershed, including three in Miller Creek. “Water storage measures upstream definitely help slow the peak flow and improve downstream habitat,“ stated Wabasha SWCD director Terri Peters.

Kennedy stressed that there is a long-standing awareness and value of soil and water conservation practices among area residents. Local residents widely support reducing runoff and improving water storage issue, both to protect local waters, but also because they recognize the tremendous value in keeping the soil in place—in SE Minnesota and throughout the state. “If large scale TMDL documents, such as the Lake Pepin TMDL, call for massive reductions of sediment and nutrients across the state, I think it’s only fair that we do our part locally at the doorstep of Lake Pepin.” declared Kennedy.

According to Kennedy, the Goodhue and Wabasha natural resource agencies plan to continue prioritizing the work of containing pathogens, limiting erosion, and improving water storage throughout Miller Creek and the MRLP watersheds. They will continue talking with landowners, targeting spots where improvements are needed in the watershed, and exploring landowner incentives for conservation practice adoption. And although the CWF grant money has been spent, Kennedy stressed that there is still local money available for conservation practice implementation, adding “if anyone wants help, we’re here to help you.” Finally, Kennedy said he believes that the next big challenge for this landscape is stepping up cover crop usage. Keeping the landscape green all year round or incorporating alternative cropping systems will be “a tougher sell,” but ultimately may be a necessary strategy for effectively protecting Minnesota’s water long term.

This article is part of a larger series that investigates what we know about eight Lake Pepin tributaries. Follow us online and sign-up for our e-newsletter so you don’t miss the next release. If you have information or pictures for other Lake Pepin tributaries, please email us at: info@lakepepinlegacyalliance.org.

Other articles in the series will be listed below as they are published.