Problem Overview


Every year, a sediment load, the size of a city block filled to the height of the Foshay Tower in downtown Minneapolis, accumulates at the head of Lake Pepin. The sedimentation rate is now 10x above normal with the Minnesota River contributing a whopping 80-90% of the annual load. Sediment accumulation in Upper Lake Pepin has contributed to record boat groundings, isolated communities, and an ecological vulnerability to collapse.

The problem is not new, but it’s reaching a critical tipping point. The Minnesota Pollution Control Agency (MPCA) has determined that the Minnesota River needs to reduce its sediment load by 50% to protect Lake Pepin. The interim goal—a 25% reduction by 2020—is a year away and the progress is unsettling. From 2010 to 2016, the actual sediment reduction was less than 1%.

As upstream stakeholders struggle to make meaningful sediment reductions, conditions in Lake Pepin are getting worse. That’s why LPLA is implementing a dual approach that includes sediment reduction and local restoration. Sediment reduction is the only sustainable option, but local restoration is necessary to maintain current uses, reverse ecological degradation, and redirect sediment input to have less overall impact.


Lake Pepin is a naturally occurring lake on the Mississippi River, spanning the 26-mile stretch from Red Wing to the Chippewa River delta. With an average width of 1.7 miles, it is the widest stretch of the entire Mississippi and covers nearly 30,000 acres.  It receives drainage from four major watersheds (Minnesota River Basin, Cannon River Basin, St. Croix River Basin, and Upper Mississippi River Basin), encompassing almost half of Minnesota and parts of South Dakota, Iowa, and Wisconsin. At the end of the last glacial period, this unique natural impoundment extended even further upriver to present-day St. Paul, but sediments flowing in from upstream have been gradually decreasing the size of the lake over time. The lake is a treasured and vital natural resource, home to hundreds of aquatic plant and animal species and a globally important flyway for migratory birds. It has also become the area’s economic backbone, fueling tourism and recreation industries that support communities along both sides of the lake. Click the video and read below to learn more.

Click this video for an overview of Lake Pepin and how water quality impairments affect surrounding communities. The cover photo shows the high sediment load from the Minnesota River flowing into the Mississippi River, just upstream from Lake Pepin.

Sedimentation & Eutrophication

Although sedimentation is a normal geological process, scientists have concluded that the rate of sediment supply  to Lake Pepin has increased more than tenfold since the arrival of European settlers. It is now anticipated that the upper third of the lake will be unsuitable for recreation by the end of this century and the entire lake substantially filled within 340 years.  Without the human-induced increase in sedimentation rates, Lake Pepin would be one meter deeper and expected to provide recreational and commercial value for another 4,000 years. 

Lake Pepin is also threatened by excess nutrients leading to eutrophication and downstream impacts. Phosphorous is the limiting nutrient and excess input from the surrounding landscape has led to eutrophication, characterized by algae blooms that reduce light and oxygen thereby threatening animal and plant survival. It is estimated that the accumulation of phosphorus in Lake Pepin sediment has increased 15-fold since 1830. This eutrophication process is tightly linked with sedimentation because phosphorous binds to soil particles, which are transported together down the watersheds to Lake Pepin. Nitrogen input is also affecting local water quality with cascading impacts all the way to the Gulf of Mexico, where a large hypoxic area, or "dead zone", has formed at the Mississippi delta leading to environmental problems, such as fish kills.

The problem is driven by natural and human-induced processes throughout all of the major watersheds, which creates complexitiy as stakeholders collaborate on possible solutions. The Minnesota River Basin (MRB), however, is the main concern since it contributes 80-90% of the sediment accumulating in Lake Pepin. LPLA has partnered with government, academic, non-profit, and citizen stakeholders to raise awareness, increase scientific understanding, and implement projects to protect Lake Pepin. While most projects are directed at mitigating upstream sources of sediment and nutrients, LPLA is also leading management efforts to reverse current impacts already affecting the lake. 

Science & Policy

Map showing Upper Mississippi River turbidity impairment contributing to downstream sedimentation in Lake Pepin (red) and Lake Pepin eutrophication impairment from excess nutrients (green). These waterbodies are assessed in separate TMDLs, but jointly affect the health of Lake Pepin.

Map showing Upper Mississippi River turbidity impairment contributing to downstream sedimentation in Lake Pepin (red) and Lake Pepin eutrophication impairment from excess nutrients (green). These waterbodies are assessed in separate TMDLs, but jointly affect the health of Lake Pepin.

Lake Pepin and many upstream waterways have been placed on the US EPA's Impaired Waters List, established by the federal Clean Water Act (CWA). Once listed, the CWA requires scientific assessments to determine how much of a pollutant can enter a waterbody without it exceeding water quality standards. These scientific assessments, referred to as TMDLs (Total Maximum Daily Loads), also identify pollution sources, allocate load reductions, and establish water quality improvement goals. They essentially serve as a diet plan for a specific waterbody exceeding water quality standards.

It seems straighforward, but the process is complicated by the fact that waterbodies-lakes, rivers, streams, and wetlands-are all connected. Moreover, turbidity and eutrophication impairments are highly inter-related problems because phosphorus binds to soil particles as they travel together through the watershed. As a result, multiple TMDLs relate to the health of Lake Pepin, including: The Lake Pepin Eutrohpication TMDL (in progress),  the Upper Mississippi Turbidity TMDL, and the Minnesota River TMDL.

The MPCA must provide reasonable assurance that the load reductions are feasible, but progress in not on track: The Minnesota River contributes 80-90% of the sediment to Lake Pepin and is required to reduce its load by half for Lake Pepin to meet water quality standards. The interim goal, a 25% sediment reduction by 2020, is only a year away. See Reports for more information.