Recent heavy rains in and around the Twin Ports raised river levels and sent thousands of tons of silt into Lake Superior, muddying the waters for anglers and raising concerns from other lake lovers.

Some of the silt is from the South Shore clay banks of the big lake, but most comes from erosion from Lake Superior's tributaries, including the St. Louis River.

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The worst offender by far is the Nemadji River, which starts in Pine County and runs through Carlton County before crossing into Wisconsin and entering Lake Superior at the Superior harbor entry.

Rain events were creating a chocolate milk-like "mud line'' in Lake Superior even in May, but the mudlines have been more pronounced through June and into July as heavy rains continue to pummel the region.

Superior officially saw 9.86 inches of rain from June 1 to July 1 - more than double their usual amount for the month, including four downpours of 1.4 inches or more, according to data from the National Weather Service. In one case, more than 9 inches fell in two days just south of the Twin Ports in the Nemadji River watershed.

The muddy western tip of Lake Superior looks similar to the post-June 2012 flood that inundated Duluth, at the time considered the most mud anyone had seen in the big lake.

Indeed recent satellite photos of western Lake Superior show heavy, chocolate-milk colored siltation stretching for miles out into the big lake, especially near the Twin Ports but also along the South Shore and in Chequamegon Bay.

"Capt." Tom Mackay, who has lived surrounded by water on Duluth Park Point for 74 years and worked 32 years as captain for the Duluth Vista Fleet, said the muddy water has been unusually persistent this summer.

"I look at it every day and have never seen it this bad. Makes it pretty tough for fishing at this end of our lake.'' Mckay noted.

Jarrid Houston, a local guide who writes a weekly fishing column for the News Tribune Outdoors section, said the muddy water has "definitely has made fishing a bit more challenging,'' but that a few days without rain already has the water slowly clearing up.

Houston said the St. Louis River has been very muddy but has not seen nearly the physical flooding damage - uprooted trees, sloughing banks and huge deposits of sand and silt - as occurred in 2012.

"If I recall, after the 2012 flooding, we never even got back onto the river the rest of the summer. This year, we really never left the river,'' even during muddy periods, Houston said. "The fish are still there, just need to find what works to catch them. We got 30 walleyes on our (St Louis River) guide trip yesterday."

Lorin LeMire, a Lake Superior charter captain, said he's had to travel farther from Duluth to find water clear enough to fish in.

"It is muddy, but no need to panic, just need to adjust,'' he said, adding that fishing for lake trout and coho salmon has been very good along the clear/muddy water line off shore from Knife River to Two Harbors.

According to a U.S. Geological Survey study, the Nemadji River has the highest sediment load of any Lake Superior tributary in Minnesota or Wisconsin - about 131,000 tons of clay silt every year. There's likely more in years with heavy rain events. That's the equivalent of 16 big dump truck loads of clay unloaded into Lake Superior every day, all year long.

All that silt clouds the big lake for miles out from river mouths, raising water temperatures (dark water absorbs more warmth for the sun) and can even coat underwater spawning beds for trout. The Minnesota Department of Natural Resources this week reported water temperatures in the 60s in the muddy areas of Lake Superior but just in the 40s in the clear water farther out from shore.

It's not just an environmental concern. Nearly every year the U.S. Army Corps of Engineers must dredge about 33,000 tons of clay out of the Superior harbor, where the Nemadji flows into the lake, just to keep access open to the Superior waterfront, including the Burlington Northern ore docks.

The clay and sand along the Nemadji, left by glacial Lake Duluth centuries ago, are a fragile base for an ecosystem much more prone to erosion than the nearby St. Louis River, which runs through more rocky and boggy country. While sediment core samples at the river's mouth show scientists that the Nemadji has always been sending some clay to Lake Superior, it's clear that the amount of clay has increased in the past 130 years. That's when large-scale logging and farming started to affect the river's 433-square-mile watershed in Carlton, Pine and Douglas Counties along the Minnesota-Wisconsin border.

Farming, development and roads all help speed the flow of water across that exposed clay and into the Nemadji system. And it appears that early logging of pines along the river's often steep banks exposed the red clay to more and more severe erosion in the form of large slumps of clay that fall into the river during rainstorms.

Efforts to curb the erosion started in the 1970s with the Red Clay Project. They expanded in the 1990s and continue today with a focus on planting trees to slow water runoff 60 miles and more upstream from Lake Superior.

The problem isn't unique to the Nemadji, however. Up the South Shore of Lake Superior clay banks are the predominant feature, often slumping into the water. In Chequamegon Bay, sedimentation is considered one of the most pressing water quality issues by the Chequamegon Bay Area Partnership, a coalition of agencies, nonprofit groups and educational institutions. The group is focusing on Fish Creek for watershed restoration efforts. The creek near Ashland sends tons of clay into the bay of Lake Superior after big storms, as is seen in the recent satellite photos of the lake.