MPCA study: Lake Pepin close to meeting water-quality standard, more work needed upstream

Contact: Cathy Malakowsky, 507-383-5949

Lake Pepin in southeast Minnesota is close to meeting its custom water-quality standard designed to minimize algae, with more work needed upstream to meet the goal, according to a study recently released by the Minnesota Pollution Control Agency (MPCA). The study focuses on phosphorus levels in Lake Pepin and the Mississippi River upstream, from the Crow River near Dayton, Minn. to the St. Croix River near Hastings, Minn.

The study also references the need to reduce phosphorus in several other rivers, including the Minnesota and Cannon rivers. These river systems are addressed in separate studies.

Phosphorus comes from many sources, including wastewater discharged by communities and industries, and runoff from farm fields and urban areas. Both urban and agricultural sources need to reduce the phosphorus they send to rivers and eventually Lake Pepin. About two-thirds of the algae in Lake Pepin are produced upstream. As such, the study calls for reducing phosphorus from upstream rivers by 10-50 percent.

Lake Pepin, which has characteristics of both a lake and river, is about 21 miles long and one of the widest parts of the Mississippi River. Nearly 50,000 square miles – roughly half of Minnesota plus a bit of three neighboring states – drain to Lake Pepin through the Upper Mississippi, St. Croix, and Minnesota rivers. Eighty-two percent of Minnesota residents live in this basin. No other water-quality project in Minnesota has addressed such a large area.

Algal blooms were once common in the lake with some leading to fish kills. Minnesota listed it as impaired —meaning it failed to meet water-quality standards — in 2002 because of high nutrient levels. The Lake Pepin study, called a total maximum daily load (TMDL), determines how much phosphorus the lake can receive and still meet water quality standards. TMDLs are part of the federal and state effort to monitor lakes and streams, identify impaired waters, and plan for their restoration.

Sediment – soil and other particles that cloud the water – is a related concern. The Minnesota and Mississippi Rivers carry high loads of sediment and much of it settles out in Lake Pepin. The sediment levels are so high that the upper part of the lake is filling in. Some phosphorus attaches to sediment so practices that reduce sediment, such as erosion controls, also reduce phosphorus.

The TMDL process has spanned several years, largely due to the need for more scientific work on water quality standards for the lake and rivers, as well as extensive stakeholder engagement. During the study period, the work to decrease phosphorus was ongoing. From 2000 to 2019, communities and industries upstream of Lake Pepin decreased the phosphorus discharged in their wastewater by 80 percent.

Thanks to their efforts, Lake Pepin is close to meeting its standard, though two sections of the Mississippi upstream need further reductions to meet their water quality goals and help Lake Pepin at the end of the system, as outlined in the table below.

Mississippi River water quality: Crow River to Upper St. Anthony Falls

Standard to meet Average level 2006-2014
Total phosphorus 100 micrograms per liter 113.9 micrograms per liter

Chlorophyll-a
(green pigment in algae

18 micrograms per liter 28.1 micrograms per liter
Mississippi River water quality: Upper St. Anthony Falls to St. Croix River Standard to meet Average level 2004-2010
Total phosphorus 125 micrograms per liter 182.3 micrograms per liter

Chlorophyll-a
(green pigment in algae

35 micrograms per liter 37.5 micrograms per liter
Lake Pepin water quality Standard to meet Average level 2009-2018
Total phosphorus 100 micrograms per liter 134 micrograms per liter

Chlorophyll-a
(green pigment in algae

28 micrograms per liter 27 micrograms per liter

For regulated parties, mainly wastewater and stormwater systems that require state permits, the TMDL may mean additional limits on phosphorus. However, most regulated parties have already met the goals for upstream waters and Lake Pepin.

The remaining pollutant reductions must then come from agricultural land, which makes up the majority of land use in the Minnesota River and Cannon River watersheds. But these sources are not subject to regulation. The focus will remain on voluntary best management practices that build soil health, reduce runoff, and otherwise protect water quality.

The agency will also hold an informational meeting about the study May 6 via Webex. For access details, and additional information, visit the study web page.

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 (507-206-2621), MPCA, 18 Wood Lake Drive SE, Rochester, MN  55904.