How Healthy is the Upper Mississippi River?
By Melinda Knutson
If you were asked the question, ‘how healthy is the Upper Mississippi River’, how would you answer it? Is the ‘health’ of the Upper Mississippi River getting better or worse? Should we spend scarce tax dollars to reverse damage or celebrate the wonderful resilience of the country’s largest river? Does river health vary by location? Do some river towns enjoy excellent sport hunting, fishing, and swimming in clean water and others just have invasive carp and mosquitos? How does our river’s health compare with other large rivers in the U.S. and globally? Should we replace some aging locks and dams with larger, more modern locks to improve the efficiency of commercial navigation? Where should we invest in habitat restoration improvements? What if the many stakeholders that use and love the river can’t agree on what to do next?
That’s exactly what happened in 1968 when the U.S. Army Corps of Engineers proposed replacing the locks and dam 26 at Alton, IL with a new dam and two 1200-foot locks. Funds were appropriated by Congress for implementation in 1970-1975 [1]. Environmental groups worried about the environmental impacts to the system, and they joined with 21 western railroads to file lawsuits to stop the project, contending that planners had not fully considered those impacts. The railroads were concerned about loss of revenue. Legal action in September 1974 stopped further actions, at least temporarily. In fact, no one knew what effect this construction project would have on the river system. There was little environmental data available on the current state of the system, not to mention the projected effects of two new, large locks.
Managing for Navigation and Fish and Wildlife Habitat
Starting as early as 1824, significant changes were made to the Upper Mississippi River—the navigable stretch of the river north of Cairo, IL—to facilitate commercial navigation. These modifications included snag removal, construction of wing dams, and alterations to the shoreline. The 29 locks and dams on the Upper Mississippi River, built during the 1930s and 1940s, created a 9-foot-deep channel for commercial navigation. These engineering changes have converted the River into a stairstep system of open river pools separated by dams.
The Inland Waterways Authorization Act of 1978 authorized the controversial new Locks and Dam 26. A master plan was required before construction and was completed by the Upper Mississippi River Basin Commission [1]. The1982 Master Plan evaluated navigation and ecological impacts, proposed an inventory and monitoring program, and outlined a management framework for resolving competing interests and integrating state, local, and federal responsibilities. The Master Plan noted that while substantial tax money had been spent on navigation, little money had gone toward assessing the river’s environmental health.
Perhaps the most important outcome of this influential report was that it clarified that the River would continue to be managed for two major purposes - commercial navigation (via the Army Corps) and fish and wildlife habitat (via two large national wildlife refuges and many state wildlife areas). Therefore, to make good decisions going forward, the public needs to know what the health of the River is.
Taking the Pulse of the River
The Master Plan highlights major information gaps in assessing the river’s environmental health, citing inconsistent data collection and lack of science coordination among various agencies and organizations. Monitoring methods were often fragmented or duplicative, making system-wide comparisons difficult. Slow dissemination of research and outdated monitoring techniques further hindered progress. Without a cohesive monitoring program, ongoing habitat degradation proceeded unchecked. It was difficult to balance efficient navigation with environmental quality. Past attempts at long-term monitoring had failed because there was no integrated plan or coordinating agency, and conflicting priorities among various agencies resulted in inconsistent funding.
Helping Fish and Wildlife - Habitat Restoration and Monitoring
Congress’s response to the Master Plan was the Water Resources Development Act of 1986[2]. This Act defined the Upper Mississippi River System as the commercially navigable parts of the Mississippi River above Cairo, IL, including its tributaries and the entire Illinois River, covering much of Minnesota, Wisconsin, Iowa, Illinois, and Missouri. This is a huge area, dominated by agriculture and forestry, small cities and towns, and a few large urban areas. The Act recognized the River System as a nationally significant transportation system and a nationally significant river ecosystem. It also established the Environmental Management Program—now the Upper Mississippi River Restoration Program—managed by Army Corps and implemented with federal and state partners.
“Former Congressman Steven Gunderson (Republican - Wisconsin) was instrumental in championing the whole program through Congress.” recalls Ken Lubinski, U.S. Geological Survey River Ecologist (retired), who participated in the early years of the monitoring program. “Eventually it all came together. The Basin Commission went out to all the states and got support and collected input about what should be monitored. This list was refined into the metrics that were collected under the monitoring program. After 10 years, it was determined that the program was so valuable for both habitat restoration and monitoring that permanent funding was warranted.”
“About two-thirds of the Restoration Program funding is spent on habitat restoration projects (Habitat Restoration and Enhancement Project) and one-third goes for monitoring and research (Long Term Resource Monitoring),” U.S. Geological Survey Research Ecologist, Jeff Houser explains. “The U.S. Geological Survey provides the scientific leadership for the monitoring and State agency staff collect the monitoring data, provide first-hand knowledge of the river’s condition, and contribute substantially to the analysis and interpretation of the monitoring data.”
What Have We Learned?
The Geological Survey summarized 26 years of monitoring data (1993 to 2019) from the Monitoring Program in a 2022 Monitoring Report that describes changes in river discharge, backwater bed elevations, the amount of forest area, aquatic vegetation, the fish community, and water quality indicators, to name a few measures [3]. This report provides information we need to make good decisions about lock and dam improvements, as well as for planning new habitat restorations.
The Good News and the Bad News
The report highlights both positive and negative findings. On the bright side, the upper parts of the River System (Pools 2 to 13) have shown improvements, including increased aquatic vegetation, better performance on some water quality indicators, and strong connections between the river and its floodplains due to the absence of levees. However, challenges remain: sediment is still building up in backwaters throughout the system, which reduces backwater depth and diminishes habitat quality for many species, and floodplain forests are increasingly turning into grasslands. Additionally, the lower dammed sections of the River System (Pools 14 to 26 and the Illinois River) have trouble supporting aquatic plants, display poor water quality, and native fish populations are pressured by invasive carp species.
Collaborations and Insights From Long Term Monitoring
The Monitoring Program is a major success story; it has addressed all or most of the information deficits described in the Master Plan in 1982 and the participating agencies work well together. “It’s remarkable where we are now with monitoring (compared with the 1970s), because we have a highly functional multi-agency partnership,” Houser said. “Agency staff know each other and how their agency fits into the collaborative landscape. Everyone works together to ensure that the public investment in monitoring is done well. When we host visiting scientists who are doing similar work elsewhere, they are impressed with how well our partners work together.”
Long term monitoring is difficult to sustain over years or decades. “Long-term monitoring is not particularly glamorous,” comments Houser. “In the early years, people want to know what you’ve learned, but it’s hard to interpret only 3-5 years of monitoring data. Once you have 10-20 years of data you can see how the different ecosystem components are connected and what changes are important. We now have the luxury of 30 years of data and it’s easy to show the value of that data. There really isn’t any other way to gain those insights for a large, complex system like the Upper Mississippi River.”
New Challenges in Need of Solutions
It's a well-known trope in science that the more you learn, the more questions you have. We have much more to learn about the River System and how we can best manage it. For example, one of the unresolved problems outlined in the 2022 USGS Monitoring Report is the negative impacts on native fish communities of invasive carps, especially in the lower impounded reaches of the river. Research is ongoing regarding how to prevent these fishes from spreading and how to control them where they are becoming dominant. Another problem is the loss of floodplain forests and conversion of large areas of former forest to grasslands dominated by aggressive grasses. Multiple agencies, including the U.S. Fish and Wildlife Service, the Audubon Society, the Geological Survey and the universities are collaborating to find methods for restoring floodplain forests.
“The Monitoring Program has done virtually everything that the original planners wanted, which now provides us a comprehensive look at the river ecosystem as a whole. That was the big thing missing back in the 1970s,” said Lubinski. “However, one thing the Monitoring Program can’t tell us is: are the habitat restoration projects (for example, island building) getting better and more cost-effective over time and are they providing cumulative benefits? A lot more funding would be needed to continue long-term monitoring and evaluate habitat improvements, perhaps using a method called adaptive management.”
Lubinski pointed out another missing element. “The planners envisioned eventually working with farmers on problems with runoff and downstream sedimentation. But, we didn’t even have enough funding to address all the issues in the river and adjacent floodplains.” Working collaboratively with farmers on runoff and sedimentation issues was eventually taken up in 2010 by the Fishers and Farmers Partnership [4]. This multi-agency partnership was developed under the umbrella of the National Fish Habitat Action Plan.
“The federal Natural Resources Conservation Service (formerly the Soil Conservation Service), the universities, and many state and local government agencies have worked with farmers on runoff and sedimentation issues for many decades,” said Lubinski. “What is unique about the Fishers and Farmers Partnership is that it seeks to remedy agricultural impacts to stream health at the scale of entire watersheds.”
How Healthy is the River System?
Is it now possible to assess the health of the Upper Mississippi River System with 30 years of data in hand? There is no simple answer to this question due to the large size and complexity of the River System. River health varies depending on the specific location and what you care about. Some river towns have excellent sport hunting and fishing, and sunny beaches for swimming. Other towns face challenges with invasive carp, cloudy water, or dying trees. Wherever you live, eagles and peregrine falcons fly above, and the landscape remains striking.
“The river’s complexity is a big reason why the Monitoring Program is so valuable,” said Lubinski. “The Monitoring Program helps direct future research so we can better understand the many interrelated cause and effect relationships.”
Administrative Challenges
The Trump Administration’s 2026 Budget proposed closing the Upper Midwest Environmental Sciences Center in La Crosse, where the Monitoring Program science staff are housed. In January 2026 when this article was written, Congress is working on a budget that will continue funding for the Upper Midwest Environmental Sciences Center and other similar offices, but at a reduced level. However, the closure proposal itself is a wake-up call that some members of the public question the value of investments in river science.
To interrupt or shutter the Monitoring Program when it has succeeded in meeting information needs for the River System that were identified almost 50 years ago seems irresponsible. It continues to provide valuable information needed to manage the River System into the future for navigation, recreation, tourism, hunting, fishing, bird-watching, clean drinking water, and all the other ecosystem services the largest river in the United States provides. “It’s sad that the Monitoring Program is threatened with closure when it is now well-positioned to evolve to address new issues.” said Lubinski. “You’re always going to have to keep learning because new problems keep cropping up and you can’t avoid that.”
References
Meet the author
Melinda Knutson worked for USGS and the USFWS Refuge System for 22 years, while stationed at the Upper Midwest Environmental Sciences Center in La Crosse, WI. She grew up on a farm in Houston County, MN and studied floodplain forest songbirds on the Upper Mississippi River in the 1990s. She writes about the river and the Driftless Area from her home in Onalaska, WI.
