Lake Pepin

Recent Update

On May 29, 2012, MCEA commented on the lack of reasonable assurance in the draft sediment TMDL, asking MPCA to use its existing broad authority to increase oversight impose greater restrictions on nonpoint sources. MCEA pointed out that assumptions in the TMDL run counter to current trends, and the TMDL has no clear plans to make changes that would change existing practices. The TMDL also lacks any concrete milestones or a timeline to make progress in implementing the TMDL. Unless MPCA takes significant additional action, the nonpoint source reductions required by the TMDL will not be achieved and the watershed will continue to have high levels of turbidity.

MPCA posted comments submitted on the TMDL on its website in 2013.

Even in a land of 12,000 lakes, Lake Pepin stands out from the crowd. Lake Pepin secured its spot in the annals of lake lore more than 80 years ago as the birthplace of waterskiing. And its sheer size—a couple miles across and some 20 miles long—and picturesque placement alongside limestone bluffs make it one of those places that inspires particular awe in those who visit it.

These are important reasons to protect Lake Pepin. But perhaps more important is that Lake Pepin’s health is indicative of the welfare of waters far beyond its shores. Lake Pepin, a naturally-impounded lake on the Mississippi River, has an enormous watershed
stretching over almost 50 percent of Minnesota. Restoring Lake Pepin means nursing that entire upstream area back to health as well as sending less pollution to the Gulf of Mexico.

A cleanup is desperately needed. Lake Pepin has been in crisis for years. As long ago as 1988, excessive phosphorus pollution turned the lake a slimy green and caused massive fish kills. Unfortunately, 23 years later, Lake Pepin continues to be choked with sediments and algae from phosphorus pollution.

The sediment and phosphorus loads to Lake Pepin have increased significantly over the last hundred years.

Lake Pepin Sediment Increases


(Dan Engstrom, Historical Changes in Sediment and Phosphorus Loading)

Lake Pepin Reconstructed Phosphorus Mass Balance

(Dan Engstrom, Historical Changes in Sediment and Phosphorus Loading)

In 2000, MCEA was a key player in the Minnesota Pollution Control Agency's adoption of rules that require lakes suffering from excessive phosphorus pollution to be listed as impaired and require development of a clean-up plan called a Total Maximum Daily Load (TMDL). Lake Pepin was among the first beneficiaries of the new rule when it was listed in 2002.

However, Lake Pepin suffered a setback in 2007 when the Minnesota Supreme Court overturned a lower court ruling in favor of MCEA, allow Annandale and  Maple Lake to increase the amount of phosphorus discharged into Lake Pepin's watershed by approving a new sewage treatment plant the communities had proposed.

Annandale & Maple Lake Case

MCEA opposed the permit issued by the Pollution Control Agency for the new plant on the grounds that it violated the Clean Water Act prohibition on increasing pollution to a water body already impaired by that pollutant, except in compliance with an approved Total Maximum Daily Load clean-up plan. The agency argued that because the city of Litchfield upstream was reducing the high level of pollution it released into Lake Pepin's watershed, Annandale and Maple Lake could increase theirs.

In the end, the Supreme Court decided the Pollution Control Agency had a wide latitude in interpreting the Clean Water Act, because their regulation was unclear. But in a sharply worded dissent, Justice Alan Page found the language was clear and the permit was simply wrong. The case does not "involve a scientific evaluation of technical or scientific matters beyond the comprehension of judges," he wrote. "[I]t requires only a basic understanding of the English language and elementary number usage."

However, a decision by the 9th Circuit Court of Appeals in a related case calls the Minnesota Supreme Court's Annandale findings (released five months earlier) into question. At issue in Carlota Copper v. Friends of Pinto Creek was a permit issued by EPA for a proposed open-pit copper mine that would discharge additional copper into Pinto Creek, a river that was already impaired by excess copper. The 9th Circuit overturned an earlier decision by EPA that the permit was sound - a decision the Minnesota Supreme Court relied on heavily - and indicated that the Clean Water Act made no allowances for offsetting new or expanded pollution by reducing existing discharges to already impaired waters, nor did it allow for new discharge permits to be issued for impaired waters before a TMDL had been completed. The decision was appealed to the U.S. Supreme Court, which declined to hear it.

The diametrically opposed decisions by the federal 9th Circuit Court of Appeals and the Minnesota Supreme Court is among the issues MCEA has sought to address in a petition to EPA for corrective actions in Minnesota's permitting program.

The problem created by Annandale is trading excess permitted capacity for new, actual discharges of phosphorus. Trading against this excess permitted capacity allows significant increases in discharge from new facilities while requiring no actual reductions from existing facilities. Lake Pepin is impaired by existing actual discharges, and increasing actual discharges will worsen the problem.

MCEA evaluated the point sources in Lake Pepin watershed and found that the permit capacity for total phosphorus was more than double the actual discharges in 2008.


MPCA has begun to develop rules to expand water quality trading options. In May 2011, it posted draft rules that embody this problem of allowing new and expanded discharges without requiring equal reductions in actual loads as offsets. Learn more about water quality trading here.

Meanwhile, TMDL studies of phosphorus and sediment pollution in Lake Pepin have been underway since 2005. These studies will determine the maximum amount of pollutants the lake can accommodate while still meeting water quality standards, and is the initial step in restoring Lake Pepin. MCEA serves as a stakeholder in the group working to develop the TMDL.

The draft sediment TMDL calls for reductions from the Minnesota River basin of 50 to 60 percent. Loads from most other basins will require reductions of 20 percent. The primary sources of the sediment are field erosion, streambank/bluff erosion, and ravines. The amount of non-field erosion has increased over time due to major land use changes. The primary phosphorus sources include sediment (with attached phosphorus), field runoff, and point source discharges. Many point source discharges have significantly reduced their loads in the last 25 years by implementing phosphorus treatment, which has increased the proportion of the load from nonpoint sources.

Learn more:

MCEA's 2009 comments on reasonable assurance

MCEA technical comments on the Lake Pepin Site-Specific Standards

MCEA comments on the 2012 turbidity TMDL

MPCA website for Lake Pepin TMDL

Archived presentations for the Lake Pepin TMDL

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