The Minnesota River’s unfortunate claim to fame as one of most polluted waterways in the country led to Governor Arne Carlson’s 1992 challenge to make the river fishable and swimmable within 10 years.

The confluence of the Minnesota (bottom) and the Mississippi (top) Rivers.
The Minnesota River has suffered from severe pollution problems for years, mostly due to agricultural runoff and erosion, with additional contributions from sewage discharge and urban runoff. The Minnesota River is the source of the majority of Minnesota’s contribution of nitrogen and phosphorus pollution to the Mississippi Riverand much of the pollution choking Lake Pepin.
Current phosphorus contributions to Lake Pepin:

(From Norm Senjem, The Lake Pepin TMDL: What's New?, June 4, 2009)
Current sediment contributions by basin:

(From Norm Senjem, Life Support: A Sediment Diet for the Mississippi River, May 4, 2011)
In 2002, MCEA released a report analyzing that decade long effort, concluding that Governor Carlson’s challenge had not been met.
Unfortunately, a 2011 biological assessment conducted by MPCA determined that the Minnesota River showed little improvement in supporting biological life from ten years earlier. Worse, an August 2011 study of monitoring data by the U.S. Geological Survey found that nitrate concentrations from Minnesota and Wisconsin to the Mississippi River at Clinton, Iowa increased by 76 percent between 1980 and 2008.
Minnesota River Restoration Efforts
Municipal sewage treatment plants have been doing their share to reduce phosphorus contributions to the Minnesota River since the federal Clean Water Act was passed in 1972. In 2004, the Minnesota Pollution Control Agency completed a Total Maximum Daily Load study to address the low oxygen levels in the lower 26 miles of the river, above its confluence with the Mississippi.
The TMDL found that phosphorus discharges from the 40 largest municipal and industrial treatment plants in the basin needed to be reduced by over half. These reductions are being implemented through a General Phosphorus Permit. MCEA has been involved in this process throughout, as a member of the stakeholder group overseeing the study, by commenting on the phosphorus permit and then tracking its implementation.
While these are positive steps, the Minnesota River will continue to suffer without numeric pollution limits for phosphorus and nitrogen, just like the Mississippi. In addition, the Mississippi and Minnesota Rivers will not meet healthy limits until much more is done to target and implement improved agricultural practices.
MPCA is now working on developing a clean-up plan to address the turbidity (cloudiness) of the river. The plan is expected to focus on nonpoint sources of pollution.
Learn More
Download MCEA's 2002 report, Minnesota River Clean-Up: Ten Years Later.
Lower Minnesota River Dissolved Oxygen TMDL