Mississippi River - Lake Pepin

The Mississippi River - Lake Pepin watershed includes 205,747 acres that drain several small, coldwater streams in bedrock-dominated bluff country. The largest of these streams is Wells Creek (45,954-acre watershed), which winds through 18 miles of bluff lands and joins the Mississippi near Old Frontenac, southeast of Red Wing. Hay Creek is a popular trout stream (30,405-acre watershed) that flows from south to north, joining the Cannon River bottoms at Red Wing. Three other named streams are all designated trout waters, and drain directly to the Mississippi River: Bullard Creek (10,245-acre watershed), Gilbert Creek (16,007-acre watershed) and Miller Creek (11,168-acre watershed).

This watershed is named for Lake Pepin because all the streams drain to the lake. However, this study excludes Lake Pepin, which is the focus of a separate project: Lake Pepin - TMDL project: Excess nutrients.

The Vermillion River watershed encompasses 335 square miles in central Dakota County and extreme southeast Scott County, part of the Twin Cities seven-county metropolitan area. The Vermillion River Main Stem flows 38 miles from the headwaters in New Market Township through Eureka Township, the city of Farmington, Empire and Vermillion Townships, and on to Hastings, where it discharges to the Mississippi River. Major tributaries to the Vermillion include South Creek, Middle Creek, and North Creek (winding through Lakeville and Farmington) and South Branch (through Castle Rock and Vermillion Township).

While part of the same watershed, the MPCA will study and report on the Vermillion area separately from the Mississippi River - Lake Pepin tributaries.


The Mississippi River - Lake Pepin watershed consists of forests, bluff lands, and cultivated lands. The top of the watershed is rolling cropland interspersed by many small tributaries that drop steeply through forested valleys with scattered goat prairies atop cliffs. The tributaries join to form the named streams, which drain directly into the Mississippi River. The watershed is only about 50 miles southeast of downtown St. Paul. As a result, the watershed is subject to development pressures.

Agriculture is the primary land use in the watershed (approximately 70%). About 10% of the land is in grass. Corn and soybeans make up over half the tilled acreage of the area, with barley, oats and pasture land present. Forage production is strong because of the large number of dairy cows in the region. Of the grassland, 90% is in pasture and a small percentage (<10%) is in a management intensive rotational grazing system. Most of the remaining acreage is deciduous forest. Frontenac State Park, Lake Pepin, and the coldwater fisheries are significant natural resources that provide recreation and revenue in the region.

    What's being done

    The MPCA is working with local partners to understand the complexity of the karst geology, which underlies much of the Wells Creek watershed. In karst, surface water and groundwater interchange regularly. Water flowing on the surface may suddenly drop into a sinkhole and then re-emerge a few miles downstream as a spring out of the limestone to rejoin the surface water. Because groundwater is used as a primary drinking source in the area, it is especially important to exercise caution when applying anything to the surface.

    Monitoring and assessment

    Strategy development for restoration and protection

    Implementation plans

    PDF icon Long and Farquar Lakes Nutrient TMDL Implementation Plan (wq-iw9-06c)

    The original version of the Long and Farquar Lakes Nutrient TMDL Implementation Plan was approved by MPCA on June 30, 2010. The plan was updated October 2017.