The muddy water of the Minnesota River doesn’t just look bad. High levels of sediment washing into the state’s namesake river are choking out vegetation, suffocating fish and, eventually, clogging up Lake Pepin.

It is also responsible for the bulk of the sediment polluting the Mississippi River in the state.

In a set of new reports, state pollution regulators said Minnesota must find a way to cut the river’s sediment levels in half, a 25-year undertaking they estimate will cost up to $360 million.

“Sediment is one of the biggest problems we have in the Minnesota River,” said Wayne Cords, regional manager for the Minnesota Pollution Control Agency (MPCA) in Mankato.

The sediment study is one in a series of new MPCA reports on the greater Minnesota River basin and the water draining into it that are open for public comment until Sept. 20. The reports, some focused on other pollutants and cleanup strategies, follow an MPCA study last winter that showed the river is contaminated with E. coli and fecal coliform bacteria, mainly from failing septic systems and livestock manure.

The documents paint a fresh, alarming picture of a workhorse river still under siege despite decades of effort to clean it up.

There has been some improvement in the concentration of sediment in the water, Cords said, but that’s offset by the greater volume of water now gushing down its channel. That’s because of increased rainfall from Minnesota’s changing climate, fewer wetlands and natural areas to retain rainfall, and farming practices that increase the flow of water running off the land. The result: More water is rushing down the Minnesota River, per inch of rain, than in the past.

The Minnesota River flows more than 300 miles from the South Dakota border to Fort Snelling, where it joins the Mississippi River. That takes it through the heart of southern Minnesota’s farm country: About 80% of the land in the river’s basin is used for agriculture.

Most of the sediment carried into the Minnesota River comes from three specific watersheds in the basin: the Blue Earth, Le Sueur and the Lower Minnesota watersheds — all on the river’s eastern portion. It is primarily coming from eroding ravines, bluffs and stream banks, and runoff from cropland.

The Minnesota River itself is getting wider as its banks crumble, but the smaller streams and tributaries feeding it are eroding and widening much faster, Cords said. “People that used to live hundreds of yards from a tributary are now suddenly having their back porch fall into the river,” he said.

The reports lay out a host of cleanup strategies. One of the most important, Cords said, is improving the health of the soil. That means reducing tillage, planting cover crops and adding perennial crops that hold the soil in place.

There is no one organization in charge of the cleanup, Cords said, and most of the work will be done at the local level. The $360 million will likely come from a number of sources, he said, including federal programs, landowners, the Minnesota Board of Water and Soil Resources and the state’s sales tax-financed Clean Water Fund.

“Everyone needs to be doing something,” said Cords.

A farmer tries strip tilling

Conservation groups, however, said addressing the sediment overload will require a drastic shift in the state’s farm practices to hold more water back on the land. The drumbeat is getting louder for a plan that encourages landowners to move from annual row crops such as corn and soybeans to a perennial cropping system with plants such as the wheat-like grain Kernza, or perennial oilseeds and legumes.

But at the moment, markets for perennial crops aren’t big enough to make the switch economically viable for farmers, said Trevor Russell, water program director for Friends of the Mississippi River. The public, policymakers, farmers and industry need to come together to build the markets and supply chains, Russell said.

“Our hope is in maybe 10 to 15 years, if we can establish robust markets, we could start to see these crops on the landscape at scale,” Russell said.

Greg Entinger, who grows corn and soybeans on his farm near New Prague, said he would plant perennial crops if he could sell them. In the short term, he has taken steps to address the erosion he was experiencing on his land. The MPCA showcased Entinger’s farm Thursday as it certified him for conservation work as part of the Minnesota Agricultural Water Quality Certification Program.

One of the new practices Entinger showed off is strip tilling, which leaves an untouched band of soil between rows of cops that can catch and slow water. He had to buy an expensive new strip-till rig to do it, he said in an interview, but it’s made a difference, along with drainage basins and special inlets that screen out sediment in areas with drain tiles. It’s all holding water back, he said.

“This is new to this area and a lot of people said, ‘It won’t work, it won’t work,’ ” Entinger said. “Now they’re starting to recognize it. I haven’t lost yields. I see my soil being healthier. It feels better.”