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After years of complaints about tainted drinking water and weed-choked waterways, proposals for tighter state restrictions on industrial-scale dairy operations are in the works, the Department of Natural Resources disclosed in a letter appended to a 124-page audit report that was released earlier this month.

But clean-water advocates weren’t celebrating. Last week they were still digesting the audit findings, which raised new doubts about Wisconsin’s ability to enforce laws protecting its drinking water, lakes and streams from the manure the dairy industry generates.

One leading lawmaker is worried that without adequate law enforcement, the state could slide back toward the polluted conditions that existed before enactment of the federal Clean Water Act in 1972, and he’s not sure the Legislature is prepared to make needed changes.

State Sen. Robert Cowles, who initiated the audit in his role as co-chairman of the Legislature’s audit committee, wants laws changed so more of the fee revenue the DNR collects from polluters stays with the department to pay for more enforcement staff.

The Green Bay Republican said Wisconsin residents have a right to be upset about the report compiled June 3 by the nonpartisan Legislative Audit Bureau that detailed shortcomings in the DNR’s enforcement of laws limiting water pollution.

“My constituents who saw the story wondered ‘What the heck is going on?’ ” Cowles said. “The people of this state believe in water quality. We brag about our lakes and rivers and having great places to fish in and swim in.”

The audit provided the clearest picture to date of deficiencies raised previously by conservation advocates and the federal government about DNR environmental enforcement, inspections and the writing of permits aimed at limiting pollution from sewage treatment plants, large farms and private manufacturers.

Inadequate staffing and heavy turnover appeared to contribute to the problem, auditors said.

Cowles said more money for staff is needed and it could come from fee revenue. But it’s far from clear that Gov. Scott Walker and Republicans who have controlled the Legislature since 2011 will agree.

Agency full-time staffing has been in a general decline since at least the 1990s under both parties. Democratic Gov. Jim Doyle oversaw reductions in full-time staff in water pollution regulation programs after the 2008 recession hit. Staffing levels increased in 2011 when Walker and his fellow Republicans took control of state government, but two years later cuts resumed.

DNR leaders said they are currently reorganizing in response to elected officials who want the department to focus on an unspecified “core mission.”

The DNR collects $5 million to $7 million annually in fees from concentrated animal feeding operations, known as CAFOs, municipal sewer plants and private industry, but it typically keeps less than $90,000, with the rest going to the state’s general fund.

Cowles said lawmakers are giving their attention to fall elections, and he hasn’t been in contact with the Legislature’s top leaders about the audit. He said he would like the Legislature to provide the DNR with more enforcement dollars as soon as possible, but he isn’t confident.

Senate Majority Leader Scott Fitzgerald, R-Juneau, hasn’t read the audit and wasn’t available for comment, his spokeswoman said Thursday. A spokeswoman for Assembly Speaker Robin Vos, R-Rochester, didn’t respond to emails.

“Any specifics related to the DNR’s budget will be presented in the governor’s budget proposal next year,” said Walker spokesman Tom Evenson.

DNR spokesman Jim Dick said Friday that after the audit was completed, department employees were able to find documents indicating the agency’s performance in assuring that permit holders were in compliance with regulations may not have been as poor as it appeared in the audit report.

As the Wisconsin State Journal previously reported, auditors found no documentation that the DNR took enforcement action for months or even years in five incidents where monitoring wells showed CAFOs were contaminating groundwater with substances harmful to human health.

Auditors found violations were issued to private industry and sewage treatment plants in just 33 of 558 instances serious enough for such citations under DNR policies over the last 10 years.

Municipal and industrial dischargers submit monthly electronic monitoring reports that DNR uses to identify violations, but auditors said when it came to CAFOs, problems with DNR record-keeping made it impossible to determine how often violations led to enforcement action.

CAFOs are expected to notify the DNR if they spill manure or apply it to fields in a way that endangers groundwater or threatens to run off into streams and lakes where it can cause beach closings and unnatural growths of weeds and algae. Violations also can be discovered through citizen complaints and DNR inspections.

The DNR has increased the number of CAFO inspections it conducts, but often their value was questionable because they were performed so far in advance of — or in some cases after — a permit was renewed, auditors said.

And even after average annual inspection numbers peaked from 2010 to 2014, fewer than half of the large livestock feeding operations were being inspected twice during each five-year permit term, the goal the state set for itself.

In a letter responding to the audit findings, DNR Secretary Cathy Stepp said the department is reducing that goal to once every five years to mirror the less stringent national standard recommended by the U.S. Environmental Protection Agency.

The change may mean fewer opportunities for the department to have contact with permit holders and, when there are problems, learn about them early enough to informally obtain compliance with regulations without formal enforcement action, Dick said.

A law firm that has challenged the DNR said low enforcement standards were an open invitation to polluted water.

“Safe water is too important to bet on industries maintaining compliance even when it’s well-known that the responsible regulatory agency is inspecting less, enforcing less, and charging fewer fines when violations do come to light,” said Tressie Kamp of Midwest Environmental Advocates. “Particularly for industries like CAFOs where the permitting system is set up for self-regulation and self-reporting, add decreased state monitoring on top of that and it becomes clear that we’re just not doing enough to protect our state’s water resources.”

Stepp also disclosed a series of changes DNR has begun aimed at better protecting the aquifer that supplies drinking water to many people in places like Kewaunee County, where a shallow layer of topsoil and porous bedrock can allow manure to taint groundwater.

Pollutants associated with animal waste have been found in 30 percent of wells tested in the county, which has a high concentration of CAFOs. Last summer, after citizens groups and conservationists complained to the U.S. Environmental Protection Agency, the DNR formed a series of “work groups” — made up of farmers, other residents, conservation advocates and government officials — to study the problems.

The DNR has adopted a recommendation to set tighter restrictions on spreading of manure in places like Kewaunee County, Stepp said in the letter. Farm operators have been asked to follow the restrictions voluntarily while the department begins its rule-making process, she said. The process can take months or years, depending upon several factors, including how long the governor and lawmakers take to review the changes.

The department hasn’t decided if it will use emergency rule-making authority to speed up the process, Dick said.

State Dairy Business Association lobbyist John Holevoet said he wasn’t close enough to the work groups to be able to comment on the recommendations, but he said it’s possible some of the unfavorable audit findings are misleading.

Acting on other work group recommendations, the DNR has already begun to perform more audits of manure-spreading practices, has reallocated staff to fill CAFO program vacancies and formed internal teams to consider changes in the way the department responds when new contamination of drinking water is discovered, Stepp said.

Several recommendations from the Legislative Audit Bureau regarding CAFO enforcement noted DNR employees didn’t have time to adequately review annual reports submitted by CAFOs or plans describing how they will spread manure without polluting.

Stepp said in the letter the equivalent of 10.5 full-time employees in regional offices handle permitting and compliance duties that auditors said needed improvement. Currently, there are 31 CAFO permits for each staff member. The ratio needs to be reduced to 20-to-1 for required work to be accomplished, Stepp said. She didn’t include an estimated cost.

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Steven Verburg is a reporter for the Wisconsin State Journal covering state politics with a focus on science and the environment as well as military and veterans issues.