While the Minnesota River still has high levels of phosphorus, wastewater treatment plants have dramatically reduced their contribution to phosphorus emissions, according to the Minnesota Pollution Control Agency. Here, a pipe emptied into the river near Shakopee.

A billion dollars of effort and decades of heightened concern haven’t been enough for the Minnesota River, the Minnesota Pollution Control Agency reported last week. “Overall, the Minnesota River is unhealthy,” the agency sadly concluded after its most comprehensive assessment to date of the state’s namesake waterway, drawing from 10 years of data from 139 monitoring sites along the river’s 338-mile course.

“Sediment clouds the water, phosphorus causes algae, nitrogen poses risks to humans and fish, and bacteria make the water unsafe for swimming,” the report summarized. While acknowledging the value of recent efforts at river protection by governments and private citizens, the report says water quality remains compromised.

Why so little progress? As if on queue, the skies opened with an answer. Hours after the report’s release, unseasonably heavy storms dumped more rain on portions of the Minnesota River’s watershed region than they typically receive in a full month.

Water volume is up in the river and its tributaries, and that’s working at cross purposes with efforts to keep sediment and nutrients out. Heavier-than-usual precipitation — a predictable consequence of rising greenhouse-gas levels in the atmosphere — is one reason more water is flowing. Another: Farmers have drained water away from their fields and eliminated wetlands to boost crop production. That matters much in the Minnesota’s basin, where 80 percent of the land is used for agriculture.

The report does not hesitate to point to agriculture as it discusses the need for more remedial action: “Since that’s the majority land use, that’s where most of the work needs to be done.”

It’s also where politically charged resistance to government-imposed environmental regulations runs high. Unhappiness in farm country with DFL Gov. Mark Dayton’s push for a buffer-strip requirement along public waterways likely contributed to DFL losses in the last election.

Compliance with the buffer-strip law has been good, the state reported last week, with buffers in place along 94 percent of public waters. But buffer-strip opponents still consider the 2015 law a state land grab and argue that it affords too little room for adaptation to individual circumstances. Some argue that before city-dwellers demand sacrifices from farmers, they should do more to stem their own water contamination.

That’s been happening, the report said. A number of cities and towns in the watershed have invested in wastewater treatment upgrades at considerable cost to local taxpayers and with millions of dollars in state support. The report credits those improvements with progress on phosphorus levels — the report’s one positive note amid rising nitrogen and sediment levels in the river. Water treatment upgrades are not finished, and need to proceed. But the report says it’s increasingly clear that municipal water treatment won’t be enough to keep public waterways healthy.

Community leaders in ag-dependent southern Minnesota have been understandably hesitant to press their farmer-neighbors for costly changes for the sake of cleaner rivers and streams. But river remediation tactics can benefit farmers as well as the environment. Applying chemicals to cornfields in the summer, when plants can absorb them quickly, can both produce better yields and minimize water pollution. The MPCA report notes that building soil health is good for both farmers and water quality. University of Minnesota researchers are developing cover crops that prevent erosion as they sequester the nutrients that are an asset in the soil but a liability in the river. If that research develops cash-producing cover crops, so much the better.

The MPCA report’s sobering message is that without more help from agriculture, the Minnesota River and its tributaries will continue to lose aquatic life, lose recreational value, and pose an increasing risk to human health and community prosperity. The river’s deterioration needs to be understood as a risk to all who live near it, no matter their livelihoods.