St Louis River Estuary: The stories and the science

  • Fishing
  • The Stories
  • The Science

Nearly one-third of the St. Louis River Estuary has been filled or dredged since the mid-1850s, yet it remains one of the most biologically productive wetland complexes within the Great Lakes.

Over 45 native species of warm water fish live in the St. Louis River Estuary.

Prized walleye, channel catfish, northern pike, muskellunge, small mouth bass, black crappie and lake sturgeon live within this 12,000-acre freshwater complex of wetlands, tributary streams, and bays.

High up in the estuary, just below the Fond du Lac dam to the southern end of Nekuk Island, the river is relatively undisturbed.  Here the rocky bottom and strong currents provide spawning habitat for walleye, lake sturgeon and other fish, making it a favorite springtime haunt for anglers seeking walleye. Riverfront property owner, Kenny Danelski, jokes that “we could walk across from one shore to the other, stepping from boat to boat” in the spring. Boating requires constant vigilance in this section of the river.  Fluctuating flows from a series of upstream dams, combined with periodic water level changes caused by Lake Superior seiches bring underwater rocks and obstacles unpredictably close to the surface.

At one time the community turned away from the river, but that has changed.

Today, a visit to the river can be anticipated with pleasure, but that wasn’t the case from the mid 1950s to the late 1970s.  John Lindgren, a fisheries biologist with the Minnesota Department of Natural Resources (MDNR) and a 20-year resident says “You didn’t go into the water; it was smelly and had different colors.” 
Water quality improved dramatically after the Western Lake Superior Sanitary District Wastewater Treatment Plant (WLSSD) started operating in 1978, and today the estuary provides some of the highest quality and diversity of fishing in the region.  

  • In a 2003 creel survey, Minnesota anglers spent 100,000 more hours fishing on the estuary than on the entire North Shore of Lake Superior.
  • Lake sturgeon, an ancient and slow-growing lake fish (it takes 24 years for sturgeon to reach reproductive age) are making a comeback with the help of state and tribal biologists from Minnesota and Wisconsin. Young sturgeons were released in the estuary from 1983 to 2000, and critical habitat was restored.
  • In 2011, biologists from the Fond du Lac Band of Lake Superior Chippewa found the first young sturgeon naturally produced from the stocking that took place nearly 30 years ago!

Despite the vast improvements, problems linger, as reflected in Fish Consumption Advisories and high sediment loads.

John Fehnel, an avid fly fisherman who has built a business around the St. Louis River system notes that “The St. Louis needs people to care.” Maintaining this fine fishery for future generations will require dedication, vigilance, and persistence for, only a cast away, the estuary is also home to the largest harbor and international port on the Great Lakes.

Fish Consumption Guidelines

For more information on Fish Consumption Advisories, visit these websites:
Minnesota Department of Health - Fish Consumption Guidelines

The Stories

John Fehnel

John Fehnel is an avid fly fisherman and owner of Great Lakes Fly Company in Duluth, MN.  Read John's perspective.

Mark Howard

Kenny Danelski has lived along the the upper St. Louis River for over 20 years. Read Kenny's perspective.

John Lindgren

John Lindgren is a fisheries biologist with the Minnesota Department of Natural Resources and a 20-year resident. Read John's perspective.

The Science

GeograpyGeography and habitat have changed over the history of the reservoir. Read more.

dissolved oxygenDissolved Oxygen: a threat to fisheries since Europeans first colonized the region. Read more.

water qualityWater quality of the estuary is vital for fish helath. Read more.

Mercury Mercury contamination of the estuary impacts fish and other animals.  Read more.


Deep Map. Explore the St Louis River Estuary using this interactive GIS Map.

Deep Science. Dig deeper into sample design, water quality, bugs and plants.

John Fehnel

John Fehnel

Fantastic Fly Fishing

audio transcript

When John arrived in Duluth in 1994 he observed, “…there wasn’t much fly fishing going on…there wasn’t much fishing going on at all.”  But things have changed along the St. Louis River.  As John notes, “the word got out.” Greater and greater numbers of recreational anglers are taking advantage of the excellent fishing now available.

People Need to Care

John Fehnel is an avid fly fisherman and owner of Great Lakes Fly Company in Duluth, MN.  John also guides along the St. Louis River, where he has developed a niche as an expert on fly fishing for the warm-water fish species of the estuary. His work brings him face to face with the impacts of humans on the local environment. “Over-development takes its toll, man.  We’re the ones that see it.  The river and banks silted…it’s a real shame.”

John argues, “The St. Louis needs people to care.  I guide the St. Louis and when I come down the river and there’s beer cans on fires and worm cans…come on, people need to clean up… ”

Catch and Release is Key

John’s message of stewardship includes a commitment to catch and release.  When asked about ways to steward the resources of the SLRE, John exclaimed, “Catch and release.  It’s all about education.”

Kenny Danelski

Kenny Danelski

A Special Place to Live

audio transcript

It pays to know the river's secrets

“I’m not a very patient fisherman, if they’re not biting real good I’m thinking I could be doing this at home.”  Kenny Danelski has lived just downstream from the Highway 23 bridge for over 20 years, with a front row view of the annual hunt for walleye. “This whole area…we could walk across from one shore to the other, stepping from boat to boat,” he jokes. Kenny and his wife were well known by local fisherman.

Boat travel in this section of the river can be challenging, with rock piles just below the surface. The islands and rock piles in the river distinguish this part of the estuary from the lower, slower sandy channels near the mouth and keeps area fisherman on their toes. Kenny and his wife would try to alert fisherman to move over to the deeper part of the channel, near the shore. Those unfamiliar with the river would stay in the middle – thinking the Danelski’s were just trying to get them to slow down. Most regretted their choice as they ran up on the rocks!

A sign of river health

Mayflies returned to the river as it became cleaner in the 1980s and 1990s. Kenny recalls that the 3-day hatch could almost drive you crazy they were so thick, like an Alfred Hitchcock movie. Mayflies provide food for fish, and the many different kinds of fish found is another aspect that makes living on the river so special.“It has a variety of different fish. I caught this thing, I didn’t know if it was legal or whatever, so I called Rob Moss to find out what it was.” He found out it was a freshwater drum and decided to release it. Trout are also found nearby in Dubrois Creek, a small coldwater stream that enters the estuary through the Danelski property.

Reflecting on why he lives along the river Kenny says, “There’s always something to watch. If you love Mother Nature, this is the place to be.”

John Lindgren

John Lindgren

A changing resource

audio transcript

The river’s slow healing process

John Lindgren, a fisheries biologist with the Minnesota Department of Natural Resources (MDNR) and a 20-year resident says, The estuary has certainly gotten much better in the last 20 years.  The economics associated with that zone right next to the water is greatly improved – from people not wanting to be there to having million dollar plus houses situated around the bay.  That wasn’t the case 50 years ago.”

The past haunts

  • Contaminants from the past remain in the estuary’s sediments.
  • Fish consumption advisories reflect the presence of pollutants in the river.
  • Water continues to run off the land from development and the increase in hard surfaces (parking lots, roads, rooftops), carrying new pollutants into the estuary.
  •   The level of pollutants is higher in larger, predatory fish than smaller, short-lived, forage fish such as crappie due to the process of bioaccumulation (the build up of toxic substances in fish flesh. Toxic effects may be passed on to humans, bird, and wildlife eating the fish).

John notes that there has been a “slow healing” in the estuary, particularly for the small aquatic animals (macroinvertebrates) that rely on the benthic (bottom) habitat heavily impacted by pollution in the sediments.  These macroinvertebrates provide the base of the food web, which supports many fish species in the estuary, so their health influences the health of the fishery.

A healthy future

Cleaning up past pollution, limiting our impact on the estuary and improving water quality are vital to a healthy fishery.  “It’s a place where people come to catch 20-plus inch walleyes, and they can.” John points out that in addition to walleye, anglers encounter smallmouth bass, muskellunge, catfish and black crappies. “… we have a really diverse fishery and the quality is really high… I would challenge you to find a higher quality fishery near a quarter million people.” he says.


The geography of the St. Louis River Estuary tells a story of contamination, habitat loss, and recovery

The St. Louis River Estuary (SLRE) has a broad range of fish habitat, from the open waters of the harbor to the turbulent flow of the river downstream from the Fond du Lac Dam. Fish use this habitat fully – walleye from Lake Superior make the trip up river in early spring to spawn near the dam, attracting hundreds of anglers on the opening days of the fishing season. Northern pike and muskies are common, and the upper estuary has become popular for fly fishermen seeking smallmouth bass.

The rocky bottom and strong currents of the river from the Fond du Lac Dam to the southern end of Nekuk Island provide good spawning habitat for walleye, lake sturgeon and other fish. Boating requires constant vigilance in this section of the river: fluctuating flows from a series of upstream dams combined with periodic water level changes caused by Lake Superior seiches bring underwater rocks and obstacles unpredictably close to the surface. This part of the river has been the site of an extensive sturgeon restoration project.

Over the course of the last century, however, fisheries of the estuary have faced great changes and serious challenges.  According to William Hearding's survey of 1861, the estuary coastline that now serves as docks and slips for large ships (700 ft salties to the 1000 ft lakers) was once a series of mud flats and shallows, with floating vegetation mats that would drift in and out of the harbor. This part of the lower estuary was biologically rich, providing an important spawning habitat for fish and supporting a rich bird and wildlife community.

The shoreline and coastal wetlands of the lower estuary changed dramatically as industrial development increased in the mid-20th century. Extensive areas of wetland were converted to docks, slips and industrial sites. The image below shows the shoreline William Hearding mapped in 1861 superimposed onto a 2009 air photo of the estuary. Prominent changes to the original coastline include the creation of numerous dock facilities in Wisconsin and Minnesota, the rail yard south of Rice's Point, and the creation of Erie Pier for storing materials dredged from the harbor.

In addition to loss of habitat, the estuary has been the site of heavy industrial contamination, such as the the Interlake/Duluth Tar site at Stryker Bay, where tar from the coke ovens, coal soot, and oil all eventually found their way into estuary sediments, severely limiting fish reproduction and making fish unsafe to eat.

Recovery: Restoration of fish habitat in the lower estuary

Considerable efforts are underway to restore fish and aquatic plant habitat in the lower estuary. The St. Louis River Habitat Plan, developed in 2002 identified several sites within the estuary with significant habitat limitations. Two sites in particular, the 21st and 40th Avenue West Habitat Complexes were identified as priorities for “remediation-to-restoration” projects. These sites have been the focus of an “ecological modeling and design” process, in which biological data (vegetation, sediment types, benthic macroinvertebrates, and bird usage) collected in the field were integrated with models of wind energy, bathymetry (bottom configuration) and other environmental data to develop a predictive model of aquatic vegetation. To assess restoration options, a diverse group of stakeholders, including state, federal, tribal, environmental and other interest groups, developed a set of restoration options. Scenarios include alterations to the bottom substrate or bathymetry to provide more suitable habitat for emergent, floating-leaf or submerged aquatic vegetation beds, along with the creation of islands or break walls to disrupt wind fetch and reduce wave energy. The ecological design model is being used to predict the types and areas of different aquatic vegetation beds to be established, along with the consequent improvement for macroinvertebrate, fish, and bird habitat. This ecological design tool will provide additional information to guide restoration activities within the estuary and ultimately further the removal of Beneficial Use Impairments from this Area of Concern.

Area of Concern

The lower St. Louis River and surrounding watershed were designated an "Area of Concern" (AOC) under the Great Lakes Water Quality Agreement in 1989 because of the presence of chemical contaminants, poor water quality, reduced fish and wildlife populations, and habitat loss. Among the Beneficial Use Impairments (BUIs) identified in the AOC are Loss of Fish and Wildlife Habitat, Degraded Fish and Wildlife Populations, and Degradation of Benthos. The St. Louis River Citizens Action Committee, now the St. Louis River Alliance (SLRA), was formed in 1996 to help meet the needs of the AOC. Following the recommendations of the St. Louis River AOC Stage II Remedial Action Plan, the SLRA completed the Lower St. Louis River Habitat Plan in 2002 as "an estuary-wide guide for resource management and conservation that would lead to adequate representation, function, and protection of ecological systems in the St. Louis River, so as to sustain biological productivity, native biodiversity, and ecological integrity."

Maps and Data

Water levels fluctuate throughout the year – View recent data from the Duluth Ship Canal.

Dissolved Oxygen

What has been the biggest water quality threat to fisheries in the St. Louis River Estuary since Europeans first colonized the region?

Common answers to this question include toxic contaminants or excess sediment, but it is another water quality problem that has most affected the estuary's diverse fish communities over time.

As sediment settles out of water and onto the bottom of the estuary and the streams that flow into it, the small spaces between rocks and woody debris are filled in with mud and sand. Unfortunately, some of the insects that fish eat need those spaces to survive. Trout, which need a clean, gravelly stream bottom to spawn on, are also negatively affected when the sediment settles to the bottom. Additionally, the tiny particles of sediment can cover a fish's gills, making it difficult to breathe. Think about how difficult it would be to breathe during a dust storm.

As the estuary became an economic engine for the region because of its well-protected port and proximity to abundant natural resources, industrial activities grew, and along with this, so did the human population. As was the case in the early 20th century throughout the western world, rivers and harbors served as sewers for industrial and municipal wastes.  These organic wastes were food to the natural communities of bacteria, fungi, and small aquatic animals that ultimately decomposed most of it. Unfortunately, decomposition of the excess organic matter consumed oxygen dissolved in the water at a much higher rate than would have occurred naturally.  As more and more paper mill liquor, sawmill sludge, petroleum wastes, and human sewage was discharged, the oxygen consumption from this biodegradation eventually overwhelmed the processes that added oxygen back to the water (wind mixing and photosynthesis). The end result was very low levels of oxygen, sometimes approaching zero. This was especially true in summer, when river flows were lower (bringing in less oxygen-rich, flowing water) and water temperatures warmer (decomposition rates increase as temperature increases; warm water holds less dissolved oxygen than cold water).  Fish kills were common during these years, and the native invertebrate community (mayflies and dragonflies, for example) must have been largely eliminated, with the exception of a few hardy species.

A concerted clean-up effort paid off

Fortunately, by the 1970s the U.S. and some states (including Wisconsin and Minnesota) passed legislation to begin the long and expensive process of restoring degraded waterways, including the St. Louis River.  The first and most critical task was to address the numerous sources of organic matter finding their way into the river and harbor. About $100 million in federal funding was ultimately provided to create the Western Lake Superior Sanitary District (WLSSD). State-of-the-art wastewater collection and treatment facilities were built to consolidate 14 inadequately-treated discharges into one discharge point that met state and federal standards and provided additional pre-treatment for paper mill effluent.  Similarly, municipalities in Wisconsin discharging into the estuary have also upgraded their sewage treatment plants.

Water quality in the St. Louis River rapidly recovered after WLSSD came on-line in 1978, with dramatic increases in dissolved oxygen and greatly reduced levels of fecal coliform bacteria (an indicator of human feces) and many other parameters. This “story” can be viewed interactively by examining water quality data at many sites in the river over the period 1973-1996 using our dataviewer.

Water Quality

Water Quality

What some fish see is what they can “get”

Many of the fish in the St Louis River Estuary (SLRE), including walleye and muskellunge, are visual predators. When the water gets too cloudy they can't see their prey (or your fishing lure) very well and have a difficult time finding enough to eat. Malnourished fish struggle to reproduce and even to survive.

As sediment from eroding streambanks and stormwater runoff settles out of water and onto the bottom of the estuary and the streams that flow into it, the small spaces between rocks and woody debris are filled in with mud and sand. Unfortunately, some of the insects that fish eat require those spaces to survive. Trout, which need a clean, gravelly stream bottom on which to spawn, are also negatively affected when sediment settles to the bottom. Tiny sediment particles suspended in the water can cover a fish’s gills, making it difficult to “breathe,” just as a dust storm would make breathing difficult for us.  

The amount of suspended sediments in water can be measured in a variety of ways. The total weight of the suspended material in a known volume of water (total suspended solids or TSS) can be determined. A simple device known as a turbidity tube can be used to determine the clarity of the water. Finally, the turbidity, or cloudiness, of water can be determined by an electronic meter that measures how light passes through a water sample. The image below shows a range of turbidity, measured in units called Nephelometric Turbidity Units or NTUs.

Storm sewers bring more than water to the estuary

TSS measurements for 10 different streams that flow into the SLRE. The blue bar shows TSS levels during base flow (dry period), and the red bar shows TSS levels for the same stream during a rainstorm. Click to zoom.

TSS measurements for 10 different streams that flow into the SLRE. The blue bar shows TSS levels during base flow (dry period), and the red bar shows TSS levels for the same stream during a rainstorm.

Knowing where the excess sediment is coming from helps us focus our restoration efforts. When it rains, the natural process of erosion carries sediment from land into the water. Because of this, sediment levels in streams are typically elevated during rainstorms. Unfortunately, when we build roads, houses, parking lots and other impervious surfaces, rain runs off the land faster and with more energy. Storm sewers and drainage ditches designed to direct water quickly off developed land to local streams and lakes during rain events increase the volume and velocity of water flowing downstream, often leading to increased stream bank erosion. The sand that is applied to winter roads can be washed into the estuary or surrounding streams via storm sewers. The type of soil in the watershed is also important. The red clay that dominates many of the watersheds on the Wisconsin side of the estuary is extremely susceptible to erosion.

Mercury and PCBs in fish

The fish are back, but can we eat them?

Thirty years ago not many people would eat a walleye from the St. Louis River Estuary (SLRE) even if they could catch one. Today there is a thriving fishery, due in large part to improved collection and treatment of human wastewater and industrial discharges. Ironically, there are still reasons for concern. The estuary remains contaminated with toxic materials, including heavy metals such as mercury and chlorinated organic compounds, such as PCBs (polychlorinated biphenyls).

Contamination of sport fish was one of the major reasons for the river being designated as a Great Lakes Area of Concern (AOC) in the late 1980s. Fish tissue measurements by Wisconsin and Minnesota from 1978-1988 revealed heavy metals and chlorinated organic compounds that exceeded criteria for protecting the health of fish, fish-eating birds and wildlife, and humans. Mercury is readily accumulated in aquatic biota and biomagnifies in higher trophic levels such as fish-eating birds, mammals, and humans, where it is a neurotoxin. This bioaccumulation means that the older, larger, and more predatory fish tend to be the most contaminated.
Unfortunately, we are advised that we should not eat all the fish we catch from the estuary. In general, people are cautioned to eat just one meal a month of large walleye, carp, or catfish. Pregnant women and children are advised to avoid these fish altogether. Mercury accumulates in muscle tissue, the very part of a fish that we like to eat, so it can’t be fileted out. PCBs accumulate in fatty tissue, so careful cleaning can reduce the amount of PCBs you take in.

If we have improved SLRE water quality, where are these toxins still coming from?

Figure 1. Regression plots of total mercury (THg) vs. total suspended sediments (TSS) in four Duluth, MN trout streams. Click to zoom.

Figure 1. Regression plots of total mercury (THg) vs. total suspended sediments (TSS) in four Duluth, MN trout streams from samples collected during varying flow regimes in 2004-2006 with 95% confidence intervals. Also shown are results from Anderson, et al. (2003) from the Poplar River, located 145 km north of Duluth, MN. The Poplar regression (log THg = 0.46 (log TSS) + 0.26; r2 = 0.66) was similar to the pooled model developed from the four Duluth streams. (from Ruzycki, E.M., R.P. Axler, J.R. Henneck, N. Will, G.E. Host, 2010. Estimating mercury concentrations and loads from four western Lake Superior watersheds using continuous in-stream turbidity monitoring. Aquatic Ecosystem Health and Management Society 14(4): 422-432).

Local industrial and municipal discharges to the estuary containing mercury were largely unregulated until relatively recently, but they are not the only sources affecting current levels. Mercury is a naturally occurring element that is released into the atmosphere from human activities, such as mining, burning of fossil fuels like coal, and several other industrial uses. These activities have greatly increased global concentrations of atmospheric mercury over what was produced by natural sources (volcanoes, geothermal springs, geologic deposits and the ocean). Atmospheric concentrations of mercury have doubled over the last 150 years, adding to remaining local sources.

Most hotspots of “legacy contamination” of SLRE sediments have now been identified and many removed or buried, but eliminating fish contamination may take decades or more because of continuing atmospheric sources, technological limitations making removal difficult, and the effect of land use and disturbance on mercury availability to fish. Mercury binds to soil particles, and research has shown a tight relationship between sediment suspended in local streams and total mercury concentration (Figure 1). So, activities that cause erosion, such as road building, construction, and some forestry practices combined with storms that lead to high stormwater flows can flush soil-bound mercury into lakes, wetlands, and streams where it can then contaminate fish. PCBs and other man-made, bioaccumulative organic chemicals behave in much the same way although their properties and health effects are very different from mercury.

Controlling stormwater runoff and erosion may help reduce mercury inputs to the SLRE and Lake Superior

Figure 2. Click to zoom.

Figure 2. Lindgren, J., Schuldt, N., Borkholder, B., Howes, T., Levar, A., Olson, C., Tillman, J., Vogt, D., 2006. A study of the St.Louis River. Minnesota F-29-R (P)-25, (, accessed 26 Oct 10.

Figure 2 illustrates how closely mercury (on the Y-axis) is associated with suspended sediments (i.e., the muddiness of the water) in local trout streams and with flow in the St. Louis River Estuary.  Therefore, improvements in stormwater management by industry, municipalities, businesses, and individual homeowners should help reduce mercury contamination from the watershed.  Most persistent, bioaccumulative contaminants like mercury also tend to be attached to particles rather than dissolved in water, so would likely also be reduced with better stormwater management.

Read more:

Minnesota Health Department - Fish Consumption Guidance Wisconsin Health Department - Fish Consumption Guidance