A contentious fight over mining and its effect on wild rice has reached new heights, thanks to a recent federal investigation.

The Environmental Protection Agency says that the state's refusal to enforce a decades-old pollution rule could undermine its authority to enforce the Clean Water Act in Minnesota.

Laws passed in 2015 and 2016 that exempt taconite and other industries from a pollution rule aimed at protecting wild rice may "strike down" the state's authority to ­implement federal environmental laws, the EPA said.

It asked the Minnesota attorney general to explain by Aug. 12 just how the state can issue and enforce industrial pollution permits if its hands are tied by the Legislature.

The disagreements, laid out in letters from the EPA to the Minnesota Pollution Control Agency (MPCA), are part of an ongoing federal investigation into whether the state has a light touch on taconite mining. It was triggered by a complaint filed last year by WaterLegacy, a Minnesota nonprofit that asked the federal government to withdraw the state's power to regulate mining.

WaterLegacy argued that the MPCA failed to update permits for taconite operations, some of which expired decades ago. The permits that have been issued are weak — some companies, for example, are only required to monitor and report pollution, but not to reduce it as required by federal law.

"We have 30 or 40 years showing that the PCA can't regulate taconite," said Paula Maccabee, an attorney for WaterLegacy. "When push comes to shove, the industry influence wins the day."

Rebecca Flood, MPCA's assistant commissioner for water issues, said in a prepared statement that the agency is routinely reviewed by the EPA for how it handles permitting, and it's cooperating with the current investigation.

EPA investigators in recent months have been digging through old permits and records in St. Paul and Duluth to determine how well they comply with federal law. A final determination could be years away.

"Until EPA determines the validity of [the] petition, we will say that we are confident in our permitting and regulatory work to protect air, water, land and human health in Minnesota," Flood said.

Focus on 2015 and 2016

But now, the EPA has added a new element to the fight by zeroing in on the 2015 and 2016 laws. "Such an action may constitute grounds for EPA's determination that the MPCA's legal authority no longer meets the requirements of a federally approved program," said Tinka Hyde, director of the EPA's Region Five water division, in a June letter to top MPCA officials.

The laws negate a long-standing water quality limit for sulfate, a mineral salt produced by runoff from taconite mines and other industries. A new rule is in the works, but it will be years before it is approved and even longer before it starts finding its way into permits. Environmental attorneys, however, said that suspending enforcement of the existing standard in the meantime is a violation of federal law.

"That's a big deal with the EPA because the state is required to enforce the sulfate standard," said Kathryn Hoffman, an attorney with the Minnesota Center for Environmental Advocacy (MCEA).

Complaints like WaterLegacy's are one way that communities and environmental groups can register their frustration with state ­regulation, said Albert Ettinger, an environmental attorney in Chicago. The EPA has never withdrawn state authority. But "in almost every case in which a petition was filed, the [state] program has been fixed to some extent," he said.

That was true in Minnesota. A petition filed by MCEA on phosphorus prompted the state in 2013 to make several changes.

The sulfate rule has been an incendiary issue in Minnesota for years. It has ignited lawsuits, intense political fights, multiple state laws designed to get around federal rules, and millions of dollars in new research on the effects of sulfate on wild rice.

The current sulfate rule was established in the early 1970s based on studies by a state scientist who found that wild rice grows poorly in waters with sulfate concentrations higher than 10 parts per million.

But it was largely ignored until tribes and environmental groups began complaining to the EPA in the early 2000s. That triggered an outraged response from industry, especially the taconite companies, prompting a whole new round of research.

Now, the MPCA has proposed a new rule based on more recent studies that acknowledges that the 10 parts per million level protects wild rice. But the effects of sulfate vary depending on the water chemistry.

Under the proposed new rule, sulfate limits will only be implemented for the lakes, rivers and wetlands where wild rice is known to grow. The agency has created a list of some 1,300 wild rice waters, with another 1,000 or so yet to be reviewed.