A Dane County judge ruled this week that the Department of Natural Resources must take into account the cumulative impacts of high-capacity wells on other water resources in cases where she invalidated seven permits approved by the agency last year.

In a closely watched case, the judge said Wednesday the DNR had ample authority to set limits on well applications to protect drinking water supplies and lakes and streams that might be imperiled by heavy water use.

The case highlights a longs-tanding controversy over high-capacity wells and their impact on waterways and aquatic life, especially in central Wisconsin, where there is heavy groundwater use by vegetable growers.

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Groundwater in the region is also a source of water for lakes, rivers, streams and wetlands.

In the case of some well permits, court records show that DNR staff expressed reservations to superiors about granting a new permit to pump more water from aquifers.

The ruling comes after a major policy shift last year by the DNR, when officials said they would no longer take into account the compounding effects that large wells can have on nearby lakes and streams when reviewing permits.

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The DNR changed its stance after Attorney General Brad Schimel, a Republican, said in a legal opinion that the agency did not have the authority to place conditions on farms and others developing large wells — even if the wells could harm state waters.

Schimel said that a 2011 law prohibits state agencies such as the DNR from placing conditions on people and businesses unless it is spelled out in state law or in rules approved by the Legislature.

At the time that Act 21 was approved by the Republican-controlled Legislature, supporters said the aim of the law was to make sure that "un-elected bureaucrats" were not not assuming power they did not have.

However, Judge Valerie Bailey-Rihn ruled the DNR had sufficient power to consider environmental impacts of wells. She cited the state's Public Trust Doctrine, which confers authority to the DNR to protect waterways.

She also cited a landmark state Supreme Court decision involving the Village of East Troy in Walworth County and the impact a municipal well would have on Lake Beulah. The justices in a 7-0 decision said the DNR had the duty to consider the impact of a large well on the state waters.

The Wisconsin Water Alliance, a recently formed group, said the judge ignored Schimel's opinion and predicted the case will be overturned. "This is an ill-advised and seriously flawed decision," the group said in a statement.

The ruling was a victory for Clean Wisconsin, an environmental group, and the Pleasant Lake Management District of Coloma in Waushara County.

Clean Wisconsin applauded the decision. A spokesman for the DNR said the agency had no immediate comment because it was reviewing the ruling.

"These huge high-cap wells pump millions of gallons of water every day, in an area of the state where streams are drying up and lakes levels are falling," said Katie Nekola, general counsel for Clean Wisconsin, in a statement.

"Water is not infinite; it's DNR's job to manage water withdrawals so that a few users don't take more than their share," Nekola said.