Mississippi River - Lake Pepin

Watershed at a Glance

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-Lake Pepin tributaries.

Hydrologic Unit Code:07040001
Intensive monitoring start year:2008
Major lakesMajor rivers and streams
There are no major lakes in the watershed; however the watershed is adjacent to Lake Pepin.
Vermillion River, Wells Creek, Hay Creek, and other small streams which drain directly to the Mississippi River.


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.

Vermillion River

The Vermillion is a slow-flowing prairie river, making its way through agricultural, suburban, and small urban areas. Approximately 49 miles of the Main Stem and tributaries on the western half of the river are Minnesota Department of Natural Resources Designated Trout Streams.

The watershed is within the Western Corn Belt Plains ecoregion. The northwestern portion of the Watershed is located in the Eastern St. Croix Moraine, and the southwestern portion of the watershed is located in the Prior Lake Moraine. Moraines are masses of rocks, gravel, sand, clay, etc. carried and deposited directly by glaciers). The Eastern St. Croix Moraine and the Prior Lake Moraine mark the limit of the former Superior Lobe and Des Moines Lobe, respectively (lobes are finger-shaped glaciers that develop at the edge of continental ice sheets). Moraine areas consist of rolling to steep hills and closed depressions where lakes and wetlands are common. The sediments of moraine areas are a complex assortment of till (a mixture of sand, silt, clay, pebbles, cobbles, and boulders), silt and sand lenses, and sand and gravel deposits. The till of the Superior Lobe is red and has a coarse texture (sandy loam). The till of the Des Moines Lobe is gray to yellowish brown and has a fine texture (loam).

The bedrock units underlying the watershed are sedimentary rocks (formed by the deposit of sediment) of marine origin. The watershed is on the southeastern edge of the Twin Cities Basin and the rock in the watershed dips toward the north and west. The dominant structural features in the watershed associated with the Twin Cities Basin are the Vermillion Anticline (a fold, convex upward) and the Empire Fault. Both the anticline and the fault are oriented geographically from the northeast to the southwest almost parallel to the course of the modern Vermillion River. These structural features are not expressed on the land surface, but can be seen in bedrock outcrops along the Mississippi River bluffs above the city of Hastings.

The predominant land use pattern in the watershed is agriculture, interspersed with suburban areas and smaller urban growth centers. Growth in the area has resulted in increased urbanization of the northwest portion of the Watershed. Parts of Burnsville, Apple Valley, Rosemount, Lakeville, and Farmington have dense residential, commercial, and industrial land use. All of Burnsville and Apple Valley and portions of the other four cities are included in the Metropolitan Urban Service Area (MUSA). As such, metropolitan services and facilities are or will be provided. Areas of urban growth beyond the MUSA boundary are evident in Lakeville, Farmington, and Hastings. Local controls in these cities provide planned growth in an effort to ensure the compatibility of land use types and the efficient use of public services and facilities.

    What's being done

    The MPCA is planning to work with local partners to:

    • Further understand the biology of Wells Creek. Intensive watershed monitoring (IWM) was completed in 2008. Follow-up monitoring and stressor identification are subsequent steps in a comprehensive approach to understand Wells Creek and its watershed.
    • 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.
    • Empower the relatively small population to implement best management practices to reduce pollutants.
    • Protect the diverse landscape of the watershed, which varies from rich farmland to karst features to bluffs with dramatic valleys. Ensuring that aquatic life and aquatic recreation are protected is important to the economy of the watershed.

    Strategy Development reports

    Monitoring and assessment reports and data

    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 New plan was updated October 2017.

    What is a watershed?

    Illustration showing contour of land directing flow of water

    Learn the basics of a watershed.

    Christoper Klucas, Vermillion River-MPCA Coordinator


    Goodhue County SWCD

    104 E 3rd Ave
    PO Box 335
    Goodhue, MN 55027

    Vermillion River Watershed Joint Powers Organization

    14955 Galaxie Avenue
    Apple Valley, MN 55124

    Wabasha County SWCD

    611 Broadway Ave, Suite 10
    Wabasha, MN 55981

    Twin Cities Metropolitan Area watersheds

    There are 33 watershed districts (WD) and watershed management organizations (WMO) in the Twin Cities Metro Area. These metro watersheds are in 8 major (8-digit) watersheds: the Rum River, Lower St. Croix, Mississippi River (Twin Cities), Mississippi River (Lake Pepin), Minnesota River (Shakopee), South Fork Crow River, North Fork Crow River, and Cannon River watersheds. These WDs/WMOs are formed and regulated by MN Rules Chapter 8410.

    A number of Total Maximum Daily Load (TMDL) Studies and Implementation Plans have already been completed or are underway for impaired waters in metro watersheds. Moving forward TMDL studies will be done in conjunction with watershed restoration and protection strategies (WRAPS) reports, which will contain the needed implementation strategy elements. Metro WRAPS will follow the timing and guidance of the watershed approach, but note that these will be completed at the metro WD/WMO scale.

    MPCA staff also review metro watershed management plans that are developed by watershed districts and watershed management organizations.


    A list of MPCA staff contacts by metro watershed is available on the Twin Cities Metro watersheds page.