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The shallow pools and dried-up tributaries of the Minnesota River will offer a rare glimpse into the phosphorus pollution that cities and towns have been releasing into the river through their sewage systems.

Phosphorus tends to become more harmful in shallow, stagnant waters, and it's been decades since a drought has caused the Minnesota River to run as low as it did this year.

That's given pollution regulators their first chance since 2012 to find out if the phosphorus pumped into the river from more than 140 wastewater treatment plants is harming aquatic life, depleting oxygen or allowing toxic bacteria to thrive when the river is low.

"When there is a lot of water in the streams, it gets more diluted and rivers have more of an ability to flush pollutants from themselves," said Glenn Skuta, watershed division director for the Minnesota Pollution Control Agency (MPCA). "It's when they're hit by lower flows, like this, that there can be a problem if wastewater treatment plants are discharging too much of something like phosphorus."

The majority of phosphorus pollution comes from fertilizers and agricultural runoff. But that's really only a problem when there is enough rain to wash the fertilizers from crop fields into rivers and streams. During severe droughts, runoff is drastically reduced and, instead, just about all the phosphorus that makes it into a river comes from the continual discharges of wastewater treatment plants, Skuta said.

In the late 1990s, phosphorus pollution started becoming more of a concern. The problem mostly has to do with oxygen. In warm waters, with enough sunlight, excess phosphorus will allow more algae and harmful bacteria to grow. Those bacteria use up oxygen, which is already limited in the summer when water temperatures are high.

Without enough dissolved oxygen in the water, insects and fish begin to die. Outbreaks of cyanobacteria — which gather in toxic clouds that look like an oily algal bloom and can kill pet dogs, hospitalize swimmers and close beaches — become more common.

Even though more phosphorus comes from agriculture, the phosphorus from wastewater treatment plants brings its own concerns. Unlike phosphorus pollution from runoff, the phosphorus from treatment plants is already dissolved when it's released into a river, said Lee Engel, who supervises the water quality monitoring unit for the MPCA.

"Because it's dissolved, bacteria don't need to break it apart from a particle to use," he said. "It's there and ready to go."

In 2004, the state set a goal for wastewater plants to cut the amount of phosphorus they discharge into rivers by 40%. Upgrades were made. New limits were set. The treatment plants made those reductions. In 2015, the state set stricter standards to prevent downstream algae blooms.

After a string of years with record rainfall, including 2019, which was the wettest ever recorded in Minnesota, there have been few opportunities to find out if those cuts were enough to protect rivers when they're low.

That changed this summer. Extreme drought cut the August flow of the lower Minnesota River to 540 cubic feet per second — down from its average of about 1,250 cubic feet per second.

The MPCA took samples along a 22-mile stretch of the Minnesota — from where it meets the Mississippi River in St. Paul to Shakopee — while river levels were at their lowest. The samples will tell if the river still had enough oxygen to support insects and other aquatic life. The results will be ready in November, Skuta said.

"It's like we're taking a pulse to see where we're at," he said. "This could verify our permit limits and show us that we're holding steady or it could tell us we're not there yet."

The state's goal is to keep the Minnesota healthy enough to support life even if its flow were to drop to 300 cubic feet per second, which would likely take a yearslong drought.

The Minnesota River has been bouncing back from the drought relatively quickly.

Its flow in September has been near its long-term average thanks to steadier rainfall over the past several weeks.

The drought has been showing signs of easing up throughout much of the southern half of the state. Over the past three weeks, nearly all towns south of St. Cloud have gotten enough rain for the U.S. Drought Monitor to downgrade them from "severe drought" to "moderate drought."

Northern Minnesota, however, remains in extreme or exceptional drought — the most severe classifications — especially near Lake of the Woods, International Falls and in Beltrami County.

It will take multiple seasons of above average rain and snowfall to bring northern Minnesota out of the drought, said Paige Marten, a meteorologist for the National Weather Service.

"It's looking to persist through the winter and into the spring," Marten said. "There are some small improvements as storms come and go. But given the severity of this drought, what's needed now is consecutive seasons of above-normal rain and snow events."

Greg Stanley • 612-673-4882