Restoring Minnesota’s Impaired Waters

What are “impaired waters”?

  • Under the federal Clean Water Act, water bodies are considered “impaired waters” when they have more pollution than allowed by state water quality standards.
  • The Clean Water Act requires states to update their list of polluted lakes, streams, and rivers every two years. Minnesota’s current list of impaired waters can be found here.
  • Once waters are listed as impaired, the Clean Water Act requires states to study and implement a plan to bring the waterbody back in compliance with water quality standards. That plan is called a Total Maximum Daily Load (TMDL) study.
  • State permits must then set limits on the concentration and “load” (total amount) of pollutants allowed and use best management practices to restore impaired waters.
  • The U.S. Environmental Protection Agency (EPA) has authority to review and either approve or disapprove a state’s impaired waters list or TMDL as well as to review federal water pollution (NPDES) permits.
Photo by Joey Rozier.

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

The Minnesota Pollution Control Agency (MPCA) has a list of more than 6,000 waterbodies impaired for the “beneficial use” of that waterbody for drinking water, aquatic life, safe consumption of aquatic life by wildlife and people, recreation, or the production of wild rice.

For Minnesota waters to be protected, the following steps all need to occur:

  1. Identify the beneficial use of the waterbody (i.e. drinking water or wild rice),
  2. Test to determine if pollution exceeds water quality standards,
  3. List the waterbody as “impaired” under the Clean Water Act,
  4. Study what needs to be done to restore the waterbody (TMDL and load allocation) to compliance with water quality standards,
  5. Control pollution and use other management practices to attain compliance.

Wild Rice Waters

Political pressure from mining companies and other polluters has been a significant obstacle to identifying wild rice waters as well as listing wild rice waters impaired as a result of excessive sulfate. WaterLegacy allied with tribes for more than a decade to secure the following results:

  • In 2021, the U.S. Environmental Protection Agency (EPA) overturned MPCA’s refusal to list any wild rice waters impaired due to sulfate exceeding Minnesota’s 10 parts per million water quality standard. EPA designated 33 Minnesota wild rice waters as impaired due to sulfate exceedance.
  • In its 2021 decision, the EPA also ruled that a Minnesota 2015 Session Law purporting to prevent MPCA from listing wild rice waters impaired due to sulfate was invalid under the federal Clean Water Act.
  • Since 2022, the MPCA has added wild rice waters impaired due to sulfate exceedance to Minnesota’s Impaired Waters List. MPCA’s 2024 draft impaired waters list included 55 wild rice waters impaired due to sulfate.

Read EPA’s 2021 decision requiring Minnesota to list wild rice impaired waters.

Read WaterLegacy’s advocacy to EPA to require Minnesota to list wild rice impaired waters and to include specific waters as impaired.

WaterLegacy also allied with tribes for more than a decade to pressure MPCA to identify waters producing wild rice. Initially, MPCA claimed that the agency could only consider the 24 wild rice waters adopted in rules (Minn. R. 7050.0470) as wild rice waters. In the 2018 wild rice rulemaking, MPCA admitted that there were at least 1,300 Minnesota wild rice waters.

  • In 2023, MPCA finally produced an evidence-based list of approximately 2,400 wild rice producing waters.
  • MPCA has acknowledged that “wild rice producing waters” must include waters that do not fully support the beneficial use of wild rice for consumption by wildlife or humans due to pollution but demonstrate the potential to attain the beneficial use in the future.

Read the Administrative Law Judge decision preserving the wild rice sulfate standard and the likely number of wild rice waters to which it applies.

Review MPCA’s online listing of wild rice producing waters developed in 2023.

Sulfate, Excessive Nutrients, and Mercury Contamination of Fish

Sulfate pollution from mining, coal plants, corporate agriculture, and other sources affects entire ecosystems, as well as the people and wildlife that depend on wild rice for sustenance.

Sulfate increases excessive nutrients that cause algae blooms and toxic mercury contamination of fish. Sulfate may double the release of phosphorus, nitrogen, and mercury from sediments and may increase the formation of methylmercury six-fold.

Schematic prepared by Amy Myrbo, PhD, working with Friends of the Boundary Waters and with WaterLegacy

Read A. Myrbo, et al. Increase in Nutrients, Mercury, and Methylmercury as a Consequence of Elevated Sulfate Reduction to Sulfide in Experimental Wetland Mesocosms (2017)

Methylmercury is the type of mercury that biomagnifies in the food chain and harms wildlife and humans who eat methylmercury-contaminated fish. The concentration of methylmercury in fish at the top of the food chain—like walleye— can be as much as 1,000,000 times higher than in the water column.

Read more about Mercury and Human Health.


Mercury Impaired Waters

Walleye. Art by Timothy Turenne

As of 2024, MPCA had listed 1,699 Minnesota mercury impaired waters. This doesn’t mean that no other Minnesota waterbodies are impaired for mercury in the water column or mercury in fish tissue. It may simply mean that other waterbodies have not been tested for mercury contamination. Information on whether waterbodies have been tested for mercury in the water column can be found online. However, there is no place where members of the public can find out whether a lake or stream has been tested for mercury in fish tissue.

Testing and Listing of Mercury Impaired Waters

WaterLegacy advocated that MPCA test for and list mercury impairments in waters that would potentially be impacted by the PolyMet NorthMet mine. Since 2014, MPCA has added the following waters near the proposed NorthMet site to Minnesota’s list of mercury impaired waters:

  • Embarrass River: segments from Headwaters to St. Louis River
  • Partridge River: segments from Headwaters to St. Louis River
  • Embarrass Lake
  • Sabin Lake
  • Wynne Lake

WaterLegacy believes the MPCA should also test for mercury in the water column and in fish in areas that would potentially be impacted by a Talon Metals/Rio Tinto mine in the Upper Mississippi and St. Croix River watersheds.

TMDL Studies and Pollution Control to Restore Mercury Impaired Waters

For most of the Minnesota waters listed as impaired due to excessive mercury, MPCA has no plan to conduct an individual waterbody TMDL study or impose conditions to attain compliance with mercury standards. That is because MPCA calculated based on the level of mercury in those waterbodies some years ago that complying with Minnesota’s 2007 statewide mercury air emissions TMDL would reduce mercury contamination of fish to levels that comply with Minnesota water quality standards by 2025.

This prediction must be validated. Factors such as sulfate pollution and alteration of wetlands hydrology have been shown to exacerbate the effects of mercury air emissions by increasing mercury release from wetlands and sediments and mercury methylation, and biomagnification in fish.

In addition to mercury air emission reductions, other regulatory actions such as controls on sulfate pollution, may be needed to ensure that levels of mercury in fish tissue are reduced so that they comply with Minnesota standards. WaterLegacy is advocating that MPCA apply current peer-reviewed science, complete TMDL studies, and implement regulatory controls to protect wildlife and human health from toxic mercury contamination of fish.

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.

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 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 all parties had agreed to was unsatisfactory.

MPCA left a million dollars of EPA funding on the table when it canceled the St. Louis River mercury TMDL study.

In 2022, MPCA again began a mercury TMDL study to analyze mercury impairments in the St. Louis River Watershed.

Slide from MPCA 2023 presentation

This time, MPCA has no governmental partners for the St. Louis River mercury TMDL, and other regulators participate as advisors. As of 2024, MPCA has chosen a model for the new St. Louis River mercury TMDL that explicitly excluded the role of sulfate in causing or contributing to mercury exceedances.

WaterLegacy submitted detailed comments and exhibits in 2023 opposing MPCA’s St. Louis River mercury TMDL methodology and advocating for a TMDL approach that included the effects of sulfate on increasing dangerous mercury contamination.

Exhibits to WaterLegacy’s comments included peer-reviewed articles on the relationship between sulfate and mercury and documentation of MPCA’s technical approach for the TMDL, which is not available online for the public to read.

  • Read WaterLegacy Comments, St. Louis River Mercury TMDL (Aug. 11, 2023)
  • Read Exhibits to WaterLegacy Comments, St. Louis River Mercury TMDL (Aug. 11, 2023)

History of 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: $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.

Present 2024

MPCA has produced no TMDL study 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.