More than half of Minnesota’s lakes, rivers and streams — including a popular stretch of the St. Croix River near the Twin Cities — fail to meet water-quality standards for protecting aquatic life and human health and are classified as “impaired.”

The St. Croix is one of 581 new waterways added to the state’s impaired waters list for 2020, due for release Wednesday by the Minnesota Pollution Control Agency (MPCA).

With the new list, the state has finished a 10-year sampling effort and now has a complete inventory of contaminated waters, a tool that can be used to track future progress in reducing water pollution.

The 3,416 waterways in the inventory show a range of problems, including excess mercury, bacteria, phosphorus, nitrate and other pollutants, as well as struggling fish and insect populations. The 3,416 bodies of water are 56% of the state’s waters; they include some well-known rivers, such as the Blue Earth and the Crow, as well as hundreds of tiny streams and creeks.

The most striking addition is the stretch of the St. Croix River from Taylors Falls south to Stillwater, which researchers found to be contaminated with phosphorus. That’s a first for the river, a national park that’s the pride of two states and widely considered one of cleanest rivers in the Midwest.

Several segments of the river were already listed as impaired for mercury and PCBs in fish tissue. MPCA scientists said they don’t know the source of the river’s phosphorus but said the watersheds feeding the river are large. Too much phosphorus — found in farm fertilizers, manure, sewage and industrial waste — can cause eutrophication, reducing the oxygen in water and choking out fish and other aquatic life. It can also fuel toxic blue-green algal blooms.

The MPCA assesses a new batch of the state’s water bodies each year and issues the report on impairments every two years under federal requirements. The latest report is a milestone for the agency, which has now assessed all 80 watersheds in the state after a decadelong effort.

Overall, the increase in troubled waters does not reflect worsening pollution, said Miranda Nichols, the MPCA’s impaired-waters list coordinator. It’s a result of hundreds more waterways across the state getting a checkup.

“It’s about knowing more,” Nichols said.

Some good news also surfaced: 14 lakes and two streams were delisted, in some cases because they’ve become cleaner. A 1.5-mile stretch of Plum Creek in Stearns County was delisted after years of work by local residents who tackled E. coli contamination. Jerry Finch, a Lynden Township resident who organized the group, said he is “thrilled” with the delisting.

Avid kayaker

The phosphorus detected in the St. Croix River is not a complete surprise, the MPCA said, because St. Croix Lake, where the river pools south of Stillwater, was already known to have phosphorus problems and deemed impaired.

Julie Galonska, superintendent of the St. Croix National Scenic Riverway, challenged the idea that the river is deteriorating. She characterized the impairment as an “administrative twist” that resulted from new standards the MPCA recently adopted for measuring large rivers.

“It’s really a response to the application of the new standards versus us seeing a huge increase in pollution,” Galonska said.

Galonska said water quality in the St. Croix has actually improved over the years, and phosphorus levels have been decreasing with better controls on wastewater treatment plants and better farming and forestry runoff practices.

The MPCA confirmed it has a new standard for river nutrient, or phosphorus, and that it was applied at the St. Croix River for the first time this year. But the river still has too much phosphorus, officials said. It remains safe for swimming, fishing and boating, Nichols said.

Greg Seitz, an avid canoeist and kayaker who founded the website St. Croix 360, called the new designation “disappointing and worrisome.”

“One of the best things about getting out there is witnessing a natural landscape and a place that feels pretty untouched by humans,” Seitz said. “I just hope it spurs some more action to change the way we use the land around there.”

The stretch includes William O’Brien State Park and the rugged bluffs that grace so many photographs. About 40 other streams in the St. Croix River basin were added to the list too, he noted, for a range of problems.

“It’s not just about the river,” Seitz said. “It’s about the whole 8,000 square miles that drain into it.”

Next: cleanup plans

About one-third of the listed water bodies are impaired for recreational use because of high bacteria in streams and phosphorus in lakes.

Nichols said that doesn’t mean you can’t swim in them. “It means you need to be careful,” she said, particularly after a heavy rainfall that flushes in contaminants.

Many lakes and streams also show problems with the fish and bug communities, an impairment not directly linked to a particular pollutant.

Mercury remains the leading contaminant of Minnesota waters, with much of it coming from outside the state — meaning a federal solution is probably required to tackle it, according to the MPCA. If mercury contamination is excluded from the inventory, only 40% of Minnesota waters are impaired.

The mercury comes from a range of human activities such as coal-burning power plants, and it travels long distances in the atmosphere and gets deposited by rain and snow. Excessive amounts in fish tissue can harm fish and the humans who eat a lot of it, particularly pregnant women and young children.

Following mercury are problems in bug and fish populations, then bacteria and sediment from erosion.

Under federal law, after waters are declared impaired, the state must study them and create a “Total maximum daily load” report, a blueprint for reducing pollution levels. The St. Croix River will be at the top of the list, Nichols said.

By 2023, the state must have restoration plans for all of Minnesota’s 80 watersheds — a task that will be made more difficult by climate change, Nichols said.

About 43 restoration plans have been approved, said Paul Gardner, administrator of the state’s Clean Water Council. The plans include measurable goals, such as the number of acres planted with cover crops or set aside, training on use of road salt and buffers created to prevent runoff.

Correction: A map attached to previous versions of this article misstated the location of Pokegama Lake.