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Travel remained difficult on many roads and highways in northeastern Minnesota on Wednesday morning due to flooding after severe thunderstorms unleashed heavy rain across the Arrowhead region and a confirmed tornado Tuesday night.

Flood warnings remained in effect across Cook, Lake, St. Louis, Itasca, Koochiching and northern Cass counties after 3 to 5 inches of rain fell across the region Tuesday. The area includes the Voyageurs National Park and the western Boundary Waters Canoe Area Wilderness along with International Falls, Duluth, Ely, Hibbing and Grand Marais.

A tornado touched down near Cotton, Minn., but no damage was immediately reported, the St. Louis County Sheriff's Office said.

The Minnesota Department of Transportation is advising motorists using stretches of Hwy. 1 between Silver Bay and Ely and Hwy. 61 between Beaver Bay and Lutsen to "drive with extreme caution" as water and debris cover portions of the highways. Motorists on Hwys. 53 and 135 near Virginia were advised to consider alternate routes, the agency said.

Flash flooding closed a tunnel on Interstate 35 in Duluth for a time Tuesday night, but the freeway was back open Wednesday morning, MnDOT reported.

"The flooding will continue overnight and may get worse before it improves," the National Weather Service in Duluth said. "Rivers and streams remain high and some continue to rapidly increase."

First responders attempted to reach a 9-year-old boy in the BWCAW who was struck in his tent by a tree that fell during the storm. A boat was used to evacuate the victim, who was rescued about 11 p.m., Cook County Sheriff Pat Eliasen said. The boy's condition was not immediately known.

In Duluth, social media posts showed water cascading onto the streets.

Dry conditions were predicted for Wednesday across most of Minnesota before another chance of rain returns Thursday and Friday, the National Weather Service said.

In the metro area, in anticipation of high water, the Minnesota Department of Transportation will close the Hwy. 41 Minnesota River crossing between Hwy. 169 and downtown Chaska at 9 a.m. Thursday. MnDOT has already called off this weekend's closure of portions of northbound Interstate 35W, southbound I-35W, and eastbound I-494 in Bloomington and Richfield due to the expected inclement weather. This closure will be moved to the weekend of June 28.

In Carver County, officials have shut down County Road 123 north of Hwy. 7 as water from the nearby Crow River covered the road. County Road 30 is closed west of New Germany to Lester Prairie, the Carver County Sheriff's Office posted Tuesday evening on X. And other roads may be, too, said Ari Lyksett, a spokeswoman for Carver County.

"We are ready to activate any needed emergency procedures in the event of high-water conditions as we monitor throughout the day and continue to receive regular updates from the National Weather Service in Chanhassen," she said.

In Delano, public works crews installed a flood wall along the east side of Bridge Avenue on Tuesday as a precaution to keep water out of the downtown area. The Crow River is expected to crest Sunday at 20 feet, about 4 feet above flood stage.

"We felt it was a good move to put it up now," said Mayor Holly Schrupp, who noted there has not been any flooding downtown. "We are taking the measures we need to take."

Officials in Mankato have closed the campground at Land of Memories Park and trails next to the Minnesota River, a city statement said Tuesday. City staff are also preparing work details for potential patrols of Mankato's levee and flood walls.

Water rose quickly along the Minnesota River from New Ulm in southern Minnesota to the south metro suburb of Savage. The rushing Cannon River and branches of the Crow River in Hennepin, Wright and Carver counties were nearing flood stage in places. Flood warnings were in place along those waterways, the National Weather Service said.

Storms traveling over the same area of already waterlogged ground could lead to flash flooding. Those living near water should prepare to immediately move to higher ground should flooding occur, according to the Department of Public Safety's Homeland Security and Emergency Management division.

The agency warned people not to park vehicles near streams or drive through flooded areas. Officials also advised not to wade through floodwaters, which can be filled with debris and could be contaminated with sewage, insects or animals.

The odds that water will recede fast are slim, said Jeff Strock, a professor at the University of Minnesota's Southwest Research and Outreach Center in Lamberton, Minn. On Tuesday, farm fields along the Hwy. 14 corridor from Waseca to the west had standing water. With the soil saturated, the water and any rain that falls will run into rivers and streams and push water higher. The long-term impact will be felt in urban areas like the metro as the glut makes its way downstream.

"The flooding situation could last for a while," Strock said.

And so could the impact as farmers won't be able to replant their crops, urban roads flood and rushing water poses dangers for venturing onto lakes and rivers.

The June deluge has "been way too much of a good thing," Strock said. "We'll feel a lot of downsides for a while."

By Tuesday morning, the storms had dropped 4.28 inches of rain in the Twin Cities, but some places in southern Minnesota have seen 3 to 10 inches of rain in the past few days.

Wet Junes are nothing unusual, assistant state climatologist Pete Boulay said.

"It's very typical," he said. "We just have not had that in the past four years. Every year the jet stream moves north. Welcome back to an active pattern."

As soggy as it has been, this June is nowhere near the wettest on record. That distinction belongs to 1874 when 11.67 inches of rain fell in June. For 2024 to crack the top 15 wettest Junes, another 2.83 inches would need to fall at Minneapolis-St. Paul International Airport, where the metro area's official weather readings are taken, the Climatology Office said.

Plagued by very dry conditions last summer, the entire state has seen adequate precipitation this year and is drought-free, according to the latest report from the U.S. Drought Monitor.