Restoring Minnesota’s Impaired Waters

What are “impaired waters”?

Under the federal Clean Water Act, water bodies are considered “impaired waters” when they contain pollution in excess of the limits set under state water quality standards. First, the Clean Water Act requires states to list polluted lakes, streams, and rivers. This list is sometimes called the “303(d)” list after the section of the Act that requires its preparation.
Once waters are listed as impaired, the Clean Water Act obligates states to study the upstream pollutants and conditions that have resulted in the impairment and determine the maximum amount of a pollutant allowed to enter a water body so that the water body will meet and continue to meet water quality standards. This is called a Total Maximum Daily Load (TMDL). Then, the state must allocate a budget for pollutants from various sources. Permits issued to discharger must restrict pollutants in keeping with the TMDL budget, and best management practices may be used to control pollution sources not covered by permit requirements.
Photo by Joey Rozier.
Under the Clean Water Act, the community can comment on a state’s impaired waters list, and the U.S. Environmental Protection Agency (EPA) has authority to review and either approve or disapprove a state’s impaired waters list or TMDL.

What’s the current status of Minnesota’s impaired waters?

The Minnesota Pollution Control Agency (MPCA) has an extensive list of impaired waters in Minnesota, which is updated every two years. The current impaired waters list can be downloaded here.

Political pressure from mining companies has been a significant obstacle to listing any wild rice waters as impaired as a result of excessive sulfate. MPCA has listed many mercury impaired waters, including some waters downstream of existing and proposed mines. The biggest challenge in relationship to mercury has been the MPCA’s failure to conduct a TMDL analysis to determine the pollutants contributing to elevated mercury in the water column and mercury contamination of fish.

Wild Rice Waters

WaterLegacy has repeatedly commented to MPCA and to EPA that MPCA must list waters that are impaired due to sulfate pollution that harms wild rice. This listing is critical to the process of analyzing and cleaning up these waters. MPCA’s failure to list wild rice impaired waters was one of many regulatory failures challenged in WaterLegacy’s petition to withdraw MPCA’s authority to issue Clean Water Act water pollution permits.

In 2011, the Minnesota Legislature passed a session law prohibiting the MPCA from listing wild rice impaired waters until rulemaking to change the sulfate standard was completed. The final deadline for completing rulemaking set by the Legislature was January 15, 2019. The rulemaking process was completed in 2018, and WaterLegacy and our allies successfully defended the wild rice sulfate standard.

Wild rice field. Photo by by Brian Bill, U.S. Fish and Wildlife Service.

Yet, as of summer 2020, MPCA has not listed a single wild rice water as impaired.

Mercury Impaired Waters

WaterLegacy advocated that MPCA list waters directly downstream of the proposed PolyMet NorthMet mine as impaired for mercury. The waters closest to the proposed tailings basin (Embarrass River upstream of Embarrass Lake and Second Creek) are still unlisted. But in 2014 and 2016, MPCA added the following impairments downstream of the proposed PolyMet project:

Embarrass River: Embarrass Lake to Esquagama Lake (mercury in fish)

Embarrass River: Esquagama Lake to St. Louis River (mercury in water, mercury in fish)

Partridge River: Headwaters to St. Louis River (mercury in water, mercury in fish)

Sabin Lake (mercury in water)

St. Louis River: Embarrass River to East Two River (mercury in water)

Wynne Lake (mercury in water)

St. Louis River Mercury TMDL

The St. Louis River is the largest United States tributary to Lake Superior. It runs through the Fond du Lac Reservation and the City of Duluth, and has a huge ecologically important estuary where it meets Lake Superior. The St. Louis River is affected by sulfate discharge from mining and impaired for mercury in water and in fish tissue along much of its length. MPCA data has shown that the level of mercury contamination in fish tissue in lower reaches of the St. Louis River is higher than it is in upstream waters.

Wall Eye. Art by Timothy Turenne

In 2011, EPA provided Minnesota with $1 million to conduct a St. Louis River TMDL study. MPCA was a key agency for this process, which also included EPA, the Fond du Lac Band of Lake Superior Chippewa, and the state of Wisconsin. The TMDL study and the plan approved by all of the TMDL participants – including MPCA – explicitly included effects of sulfate loading to the river, as well as mercury discharge.

In early 2013, MPCA abruptly pulled out of the St. Louis River mercury TMDL, claiming that the model chosen by EPA was inadequate. WaterLegacy believes that MPCA’s claims about the model are a pretext, not only because MPCA staff had previously approved the TMDL work plan, but because the plan included a suite of models that could have been adjusted or elaborated to meet any scientific concerns. In addition, records secured by WaterLegacy indicate that MPCA derailed the St. Louis River mercury TMDL after a meeting with mining staff of the Minnesota Department of Natural Resources (DNR) to discuss how the TMDL could conflict with DNR studies being done in coordination with the mining industry.

Although MPCA has since gathered information on mercury and the effects of ditched and drained peatlands on the St. Louis River, investigation of the impacts of sulfate on mercury impairments is conspicuously absent from MPCA’s updated research list.

EPA has not provided new TMDL funds. However, in 2016, with support from community members engaged by WaterLegacy, EPA enacted a rule allowing tribes that already have “treatment as a state” under the Clean Water Act to set reservation water quality standards (like the Fond du Lac Band) to also seek authority to conduct their own TMDL studies.

MPCA left a million dollars of EPA funding on the table when it cancelled the St. Louis River mercury TMDL study. Since then, MPCA has failed to research what limits should be placed on sulfate to reduce mercury contamination of fish and has not set limits on sulfate pollution of the St. Louis River. These deficits reflect the conflict between human health and mining interests.

As of summer 2020, MPCA has not restarted a St. Louis River mercury TMDL.

Failure to Conduct St. Louis River Mercury TMDL

WaterLegacy secured documents through the Minnesota Government Data Practices Act pertaining to the St. Louis River mercury TMDL. Selected dates and records are provided below:

Oct. 19, 2006

MPCA memo states that, over the next three to five years, the agency will evaluate whether sulfate discharge increases methylmercury to determine whether limits on sulfate are needed to reduce methylmercury.

April 9, 2010

A consultant report prepared for PolyMet by Barr Engineering is sent to MPCA and DNR. The report claims that elevated sulfate does not affect methylmercury.

Oct. 7, 2011

DNR proposes a coordinated DNR/MPCA effort on the mercury TMDL, stating that the coordinated plan was “accepted by the mining industry,” that money from the study comes from the mining industry and “there are no strings attached” other than the mining industry’s need “to be informed and have input on the studies to be conducted.”

The accompanying plan states that DNR has $900,000 in research money, of which $400,000 is from Environmental and Iron Ore Research programs and $500,000 is directly from mining companies. The plan proposes that DNR, MPCA, and mining company experts will direct the research and that MPCA should obtain EPA funding to coordinate with this DNR/mining industry study.

Feb. 10, 2012

After reading a posted request for proposals, the Fond du Lac Band expresses concern that mining industry personnel are involved in developing a plan for sulfate, mercury, and methylmercury research, while tribes are excluded. MPCA staff reassure DNR that MPCA is willing to “take some heat off” DNR for coordination with the mining industry in studying sulfate and mercury.

Jan. 7, 2013

MPCA signs the final Modeling and Quality Assurance Plan (QAPP) provided to TMDL partners on December 12, 2012, setting forth the process for model development and quality assurance for the St. Louis River mercury TMDL funded by the EPA.

Jan. 14, 2013

MPCA and DNR meet with the MPCA staff person who signed the St. Louis River TMDL QAPP to update him on the DNR/mining industry research. An email states that the DNR/mining industry team is “in a mid-project review” and expresses concern if the mercury TMDL “goes ahead soon”:
[T]hey are producing a lot of data and understanding which will be ignored if the TMDL mercury modeling goes ahead soon. Those scientists also seem in agreement that any modeling effort right now would produce conclusions that are almost certainly based on hubris, and such conclusions might be hard to contradict in the future.

March 12, 2013

The Fond du Lac Band writes to the MPCA Commissioner, describing three years of cooperative work with MPCA and EPA to perform a toxics TMDL for the St. Louis River that was abruptly derailed by MPCA: 
After extensive work by the contractors and partners, and outreach to other regional and national mercury experts, we were on the brink of preliminary model development and initiating a significant field data collection program for 2013 when your agency abruptly put a halt to the process.

April 11, 2013

The Star Tribune reported on MPCA’s pull-out from the St. Louis River mercury TMDL:
The state of Minnesota has abruptly pulled out of a four-year, $1 million research project to identify the sources of mercury pollution in the St. Louis River on the Iron Range, a decision that stunned the Fond du Lac Band of Chippewa and dismayed federal regulators . . .

Alie Muneer, the Chicago EPA official leading the project, said Minnesota officials had never before expressed its concerns and that she was surprised and puzzled by the suddenness and “the magnitude” of the decision . . .

She also pointed out that mercury assessments have been successfully completed on rivers in other states — some with less information than would be used in the St. Louis River assessment. As designed, it “would have produced a scientifically defensible TMDL,” she said.

Sept. 26, 2016

EPA adopted rules providing treatment of Indian Tribes in a similar manner as states for purposes of impaired waters (Section 303(d)) under the Clean Water Act.


University of Minnesota and MPCA scientific research confirms under experimental conditions that elevated sulfate in the water results in a doubling of mercury released from sediments to water and a 5.9 times increase in methylmercury.


The St. Louis River mercury TMDL has not been restarted. MPCA has produced no research or recommendations to limit sulfate loading in order to prevent mercury and methylmercury in fish impairments and the threats methylmercury in fish poses to human health.