High levels of phosphorus and recurring algae blooms caused the Minnesota Pollution Control Agency to include Lake Pepin on its list of impaired waters in 2002. Nutrient levels in the lake were too high to meet state water quality standards.

In a report released Tuesday, April 21, 2020, the MPCA found that water quality in Lake Pepin has improved and the levels are moving closer to the clean water standards.

“The MPCA is tasked by the Environmental Protection Agency to classify all the waters of the state, and according to those classifications, designate uses like boating, fishing, and swimming,” said Justin Watkins, watershed unit supervisor for the MPCA. “Then we have to write water quality standards that, if met, will support those uses.”

The report is called a total maximum daily load -- TMDL -- study and is used to determine how much of a pollutant a body of water can receive and still meet water quality standards. The study measured not only the pollutants in Lake Pepin but in upstream rivers throughout the Mississippi River watershed and compared them to a baseline set in 2000-2001.

Measuring the watershed was a massive undertaking involving many organizations and individuals. The watershed covers nearly 50,000 square miles including half of Minnesota and parts of three other states, including Wisconsin, according to Watkins.

“The TMDL really rides on upstream impairments and how they fit together,” Watkins said. “When we think about Lake Pepin, it’s kind of a report card for how things are going upsteam. If we get the river systems upstream to meet their goals, then Lake Pepin will meet its goals.”

The MPCA has regulatory control over point sources which are cities or industries that have permits to discharge wastewater into the state’s rivers and lakes. The pollution levels of those permittees are closely monitored by the MPCA. Non-point sources such as farmlands are not controlled by the MPCA and their participation in pollution reduction is voluntary.

“The TMDL regulates phosphorus reductions,” Watkins said. “The numbers have been used in cities’ permits, and we have already achieved an 80% reduction in the wastewater phosphorus load into Lake Pepin. That’s an important success story that we have already.”

The report also looked at sediment levels in the Mississippi River as it widens into Lake Pepin. Sediment is more of a concern during high flows of the river, while during lower flows, wastewater discharges are more of a concern, according to the report.

Lower flow levels can create more algae in Lake Pepin, because “when the flows are very low, water stays in Lake Pepin for a long time,” Watkins said. “A pound of phosphorus that goes into Lake Pepin during low flows can have a markedly different impact than if it were to enter Lake Pepin during high flows.”

To implement the Lake Pepin TMDL study, the MPCA is using the Minnesota Nutrient Reduction Strategy which can be seen at www.pca.state.mn.us/water/nutrient-reduction-strategy.

The agency will also hold an informational meeting about the study May 6 via Webex. For access details, and additional information, visit the study webpage: www.pca.state.mn.us/water/tmdl/lake-pepin-excess-nutrients-tmdl-project.

The MPCA is accepting written comments on the study through 4:30 p.m. June 19. Send comments to or request information from Justin Watkins at 507-206-2621 or MPCA, 18 Wood Lake Drive S.E., Rochester, MN 55904.