Waseca reported more than 10 inches from the late September gully washers that dropped multiple inches of rain across a broad area of southern Minnesota.
The town of St. Clair had major flooding. Homes, crops and roads were damaged in several areas.
But aside from the obvious damage, rivers were hit with hundreds of millions of pounds of one pollutant: sediment.
It came from farm fields, ravines and river banks that eroded because of the heavy flows, damaging water quality.
More than 200 million pounds of dirt — about 10,000 dump truck loads — poured into the Le Sueur River in the two weeks following the storms. The waterway was in the center of the heaviest rain bands.
State data show that roughly 40 percent of all the sediment measured in the Le Sueur River during the first nine months of the year came in the aftermath of the September downpour.
While this year's abundant rains one obvious factor for the increased runoff, another is the growing use of underground drainage, said Pat Baskfield, a hydrologist with the Minnesota Pollution Control Agency.
"All of these fields out here, they're underlain by subsurface drainage tile," said Baskfield, standing on the banks of the Le Sueur. "They carry a tremendous amount of water and they transport it very fast to the river systems."
Much of the sediment in the Le Sueur eventually winds up in the Minnesota River, and later the Mississippi, where sediment is blamed for filling in Lake Pepin.
There's a link between farm drainage and sediment pollution, said Shawn Schottler with the Science Museum's St. Croix Watershed Research Station.
"What we found was that in watersheds with a lot of drainage, river flows had increased more, which makes the rivers more erosive," Schottler said.
Streams in the Mankato area have widened significantly in recent years because their banks have eroded.
But the argument that agricultural drainage is to blame for increased pollution is controversial, especially in farm country.
The University of Minnesota's Satish Gupta downplayed the role of drainage.
There's no question that more soil-laden runoff is moving through the river system, Gupta said, but that's because it's raining more.
"We think river flows are up because we're getting too much water," he said.
Gupta pointed out there's been a roughly 15 percent increase in precipitation in recent decades. Heavy storms drop 37 percent more rain than they did half a century ago, according to national climate data.
Exactly which side is closer to the correct diagnosis may be less important than the solution. Baskfield argues the best way to decrease polluted runoff to rivers is through some sort of wetlands reservoir system.
Water-holding wetlands are in short supply — most have been drained and turned into farmland.
"Instead of running the water right to the rivers, it would be great to route them to wetlands where they're stored, and perhaps released at a much slower rate," said Baskfield. "When that occurs, sediment settles out."