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Phosphorus pollution from farming runoff and septic and sewer systems is steadily declining in the St. Croix River, but the nutrients continue to threaten what has long been one of the cleanest waterways in the Upper Midwest.

Overall, the river is in relatively good condition, according to a study released this week by the Minnesota Pollution Control Agency (MPCA).

Bug and fish populations are thriving. Endangered freshwater mussels — one of the strongest indicators of a healthy ecosystem — that have been wiped out of more polluted rivers across the state are still surviving in the St. Croix. And, most importantly, nearly all of the historical wetlands and much of the forest protecting and enhancing the northern headwaters of the river are still intact.

But long reaches of the river, which runs along the Minnesota and Wisconsin border, still have too much nutrient pollution from runoff and urban development to meet health and environmental standards. Mercury levels, most likely carried in from air pollution, remain high in fish. Over the past few years the MPCA has also found evidence that PFAS, harmful “forever chemicals” that don’t naturally degrade, have made it into every part of the river.

Phosphorus pollution, which causes toxic algae blooms that can kill off fish and make certain pools and lakes of the river unsafe to swim, gets worse as the river gets closer to the Twin Cities, according to the study.

While nutrient concentrations are still too high, they are lower than they were before the Clean Water Act was passed in the 1970s, said Pam Anderson, who manages the MPCA’s surface water monitoring program.

“We’re seeing an improving trend,” Anderson said. “Wastewater treatment practices have improved, and there’s been work to get better soil retention in agricultural areas to reduce runoff.”

The St. Croix was added to the list of the state’s impaired waters more than a decade ago, largely because of excess nutrients. Still, it remains one of the cleanest and most resilient major water bodies in the region. It is being used as a refuge and incubator for young river mussels to grow and mature before they are reintroduced in other parts of the state.

Remarkably, more than 90% of the wetlands that were near the river’s headwaters before European settlement are still there, according to the MPCA.

Those wetlands act like a sponge, soaking up all the excess water from the heavy rains that have caused the Mississippi and Minnesota rivers to swell and flood in recent years, Anderson said.

“The St. Croix is just not seeing those same big blowouts,” she said.

The river was also one of the first in the U.S. to be designated as a National Wild and Scenic River, which allows the National Park Service to keep a quarter-mile-wide natural buffer along much of the river’s edge.

The river’s condition remains precarious, especially as more homes, businesses and farms are built within its watershed, said Deb Ryun, executive director of the St. Croix River Association. The association released a “State of the River” study at the same time the MPCA released its findings.

“We’re cautiously optimistic that we’ll be able to keep this resource the way it has been for the last 150 years,” Ryun said. “We have to be diligent. It can tip really quickly.”

Greg Stanley • 612-673-4882