Lower Mississippi River Habitat Partnership

Project Details by Fiscal Year
2014 Fiscal Year Funding Amount
Fund Source
Outdoor Heritage Fund
Recipient Type
State Government
Start Date
July 2013
End Date
June 2018
Activity Type
Counties Affected
Project Overview

The Lower Mississippi River Habitat Partnership included three distinct project components. The U.S. Fish and Wildlife Service enhanced 700 acres of wetland and bottomland forest habitat on the Upper Mississippi River National Wildlife and Fish Refuge’s (Refuge) Root River Tract in Houston County. The Minnesota Department of Natural Resources (DNR) restored 112.7 acres of bluff prairie in Houston County; 8 acres of deep water habitat in Goose Lake (navigation pool 5 of the Mississippi River) and enhanced 200 acres of secondary channel and backwater lake habitat in North and Sturgeon Lakes (navigation pool 3 of the Mississippi River).

Project Details

Root River Tract (RRT): 

Project planning and design included site elevation surveys, development of hydrologic models and analysis of restoration alternatives.  Recommended features to restore hydrologic connectivity included: removal of existing water control structures, installation of ditch plugs and breaching of existing low level levees and dikes.   A public informational meeting to seek input on a preliminary project plan was held and feedback from that meeting used to refine project alternatives.   A draft Environmental Assessment (EA) which evaluated four alternatives for restoring/enhancing the RRT was completed and released for a 30-day public comment period in September 2015.  A public meeting to discuss the proposed project and draft EA was held in October 2015.  Responses to comments received were provided in the final EA.  A Finding of No Significant Impact (FONSI) for the preferred alternative was signed by the Regional Director, Region 3 of the U.S. Fish and Wildlife Service in January 2015.  

Restoring natural topography and drainage patterns required removal of existing dikes/levees; construction of ditch plugs using fill materials excavated from existing dikes/levees; removal of existing water control structures; and filling of an existing fish pond with materials excavated from existing dikes/levees.  Plans and specifications for completing this work were developed and local, State and Federal permits were acquired.  Work was accomplished through a combination of contracts and skilled hired labor workers in the U.S. Fish and Wildlife Service.  Heavy equipment (track trucks, backhoes, skid steers, etc.) was used to accomplish the work.  Large rainfall events in the watershed of the Root River created several floods in 2016 which affected project completion.  In September 2016, flooding on the Root River resulted in a levee breach that brought large amounts of floodwater from the Root  into the project area.  While this flooding delayed completion of some of the project features, it created a unique opportunity to observe how the project would function under flood conditions.  As a result of first-hand, on-site observations of flood waters entering and exiting the project site, project features were modified to enhance the overall hydrologic function of the project.
In 2017, installation of low water crossings at locations where trials/roads traveling through the project area crossed restored river channels, oxbows and sloughs, finishing ditch plugs, native seeding, forest enhancement (planting of hard mast trees and flood plain species) and final grading of the project was completed.  Wet conditions and high Mississippi and Root River levels delayed completion of final project features in 2017.  

The original goal for wetland and forest enhancement was to restore or enhance 700 acres.  That goal was achieved on time and under budget.  Approximately $299,612 was expended on the Root River project.  The cost of this project component was estimated at $450,000.  

Bluff Prairie Restoration: 

Bluff prairies, also known as “goat prairies” are a unique and rare habitat in southeastern Minnesota.  Goat prairies are found typically on south or west facing slopes.  Many if not most of these prairies are negatively affected by the invasion of tree species, in particular, red cedar trees.  Removal of red cedar trees as well as other trees from these prairies enhances light penetration to the vegetative layer under the trees and invigorates dormant/shaded prairie plants and seeds.  Restoring a natural fire regime through controlled burning on these sites further enhances prairie development.  Selection of prairies for restoration was based on public ownership and/or willingness of private landowners to have worked completed on their property.  Work was accomplished by contract to businesses familiar with goat prairie restoration techniques.  The original goal for bluff prairie restoration under this grant was to restore 70 acres.  The final bluff prairie acreage restored was 112.7 acres on 8 sites.  This project component was completed, on time, on budget ($150,000 spent) and exceeded the project acreage objective.

Pool 3 (North and Sturgeon Lakes) – Pool 5 (Goose Lake): 

This project component initially involved multiple habitat restoration/enhancement objectives using established large river restoration techniques such as water level management, channel modifications, island building and dredging. A “cost-share partnership agreement” between the U.S. Army Corps of Engineers and Minnesota DNR was needed to fully execute the project, however, the federally funded portion of the project was placed in deferment until the language associated with partnership agreement and future project management could be amended to satisfy legal requirements. Based on these challenges, an amendment to the accomplishment plan for Pool 3 was approved on July 10, 2015 which reduced the dollar amount of leverage expected from the Federal Government and the potential scope of the project. An additional amendment was submitted and approved in March 2016 which added Goose Lake (Pool 5) as a project site and defined that portion of the Pool 3 project to only include a channel modification at the Brewer Lake inlet. Approximately $500,000 Federal dollars were leveraged and spent on planning and development of preliminary project specifications and Environmental Assessment (EA) for the larger project. Products from this planning effort were used to develop final plans and specs and to obtain the necessary permits for the LSOH funded channel modification project. 

In 2016, 8 acres of Goose Lake was dredged to a depth of 7 feet to restore fisheries habitat. Backwater habitats are declining as a result of sedimentation. Dredging to restore depth in backwaters benefits many aquatic species by providing habitat suited for overwintering. 

Permits were secured and a contract for the channel modification project at Brewer Lake inlet was awarded in April 2017. Placement of a rock channel liner and shoreline protection was performed from barge mounted heavy equipment. Construction was completed in the spring of 2018. Pre-project monitoring of habitat conditions, fish populations and freshwater mussel populations was completed before construction. The project has achieved the desired outcome of reducing Mississippi River flows and sedimentation rates in Brewer Lake, Buffalo Slough and Sturgeon Lake. The physical and biological response expected would improve aquatic habitat conditions for fish and mussels and protection of floodplain forest communities for a variety of bird and mammal species. 

Legal Citation / Subdivision
ML 2013, Ch. 137, Art. 1, Sec. 2, Subd. 5(f)
Appropriation Language

$1,710,000 in the first year is to the commissioner of natural resources to enhance aquatic habitat. Of this amount, $450,000 is for an agreement with the United States Fish and Wildlife Service to enhance aquatic habitat in the lower Mississippi River watershed. A list of proposed land restorations and enhancements must be provided as part of the required accomplishment plan.

2014 Fiscal Year Funding Amount
Other Funds Leveraged
Direct expenses
Administration costs
Number of full time equivalents funded
Measurable Outcome(s)

Healthier populations of endangered, threatened, and special concern species as well as more common species. Remnant goat prairies are perpetually protected. Rivers, streams, and surrounding vegetation provide corridors of habitat. Improved aquatic habitat indicators.

Source of Additional Funds


Project Manager
First Name
Last Name
Organization Name
U.S. Fish and Wildlife Service
Street Address
51 E. 4th Street
Zip Code
Administered By
Administered by

500 Lafayette Road
St. Paul, MN 55155

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