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MORRISON, Wis. – All it took was an early thaw for the drinking water here to become unsafe.

There are 41,000 dairy cows in Brown County, which includes Morrison, and they produce more than 260 million gallons of manure each year, much of which is spread on nearby grain fields. Other farmers receive fees to cover their land with slaughterhouse waste and treated sewage.

In measured amounts, that waste acts as fertilizer. But if the amounts are excessive, bacteria and chemicals can flow into the ground and contaminate residents’ tap water.

In Morrison, more than 100 wells were polluted by agricultural runoff within a few months, according to local officials. As parasites and bacteria seeped into drinking water, residents suffered from chronic diarrhea, stomach illnesses and severe ear infections.

“Sometimes it smells like a barn coming out of the faucet,” said Lisa Barnard, who lives a few towns over, and just 15 miles from the city of Green Bay.

Tests of her water showed it contained E. coli, coliform bacteria and other contaminants found in manure. Last year, her 5-year-old son developed ear infections that eventually required an operation. Her doctor told her they were most likely caused by bathing in polluted water, she said.

Yet runoff from all but the largest farms is essentially unregulated by many of the federal laws intended to prevent pollution and protect drinking water sources. The Clean Water Act of 1972 largely regulates only chemicals or contaminants that move through pipes or ditches, which means it does not typically apply to waste that is sprayed on a field and seeps into groundwater.

As a result, many of the agricultural pollutants that contaminate drinking water sources are often subject only to state or county regulations. And those laws have failed to protect some residents living nearby.

To address this problem, the federal Environmental Protection Agency has created special rules for the biggest farms, like those with at least 700 cows.

But thousands of large animal feedlots that should be regulated by those rules are effectively ignored because farmers never file paperwork, E.P.A. officials say.

And regulations passed during the administration of President George W. Bush allow many of those farms to self-certify that they will not pollute, and thereby largely escape regulation.

In a statement, the E.P.A. wrote that officials were working closely with the Agriculture Department and other federal agencies to reduce pollution and bring large farms into compliance.

Agricultural runoff is the single largest source of water pollution in the nation’s rivers and streams, according to the E.P.A. An estimated 19.5 million Americans fall ill each year from waterborne parasites, viruses or bacteria, including those stemming from human and animal waste, according to a study published last year in the scientific journal Reviews of Environmental Contamination and Toxicology.

The problem is not limited to Wisconsin. In California, up to 15 percent of wells in agricultural areas exceed a federal contaminant threshold, according to studies. Major waterways like the Chesapeake Bay have been seriously damaged by agricultural pollution, according to government reports.