EDHAM, Iowa — By the time the Raccoon River winds through the western hills here, passing corn fields and livestock pens before reaching Des Moines miles to the east, it is so polluted the city has to put it through a special nutrient filter to meet government standards for drinking water.

The culprits are not industrial plants or mines belching toxins into the river. They are Iowa farms, which send fertilizer and animal wastes into the groundwater and into the river.

"Farmers are the problem," said L. D. McMullen, the general manager of the Des Moines Water Works. "And they are entirely unregulated."

The issue goes beyond Iowa. Across the country, metropolitan water agencies are battling increasing pollution from the countryside. The river pollution is spreading and helping to cause dead zones in the open seas. A recent study by the Pew Oceans Commission, an independent group examining government policies, called huge livestock feedlots and farm fertilizer runoff among the fastest-growing sources of pollution in oceans thousands of miles away.

As a result, the $171 billion, 10-year farm bill, once seen as a parochial issue for rural lawmakers, has been scrutinized by members of Congress from urban and suburban districts who realize that the upheaval in agriculture has implications beyond the grocery store.

The bill includes several proposals to reduce water pollution, like increased money to encourage farmers to practice conservation, increased money to protect wetlands, and limits on subsidies so the federal program will not underwrite further farm consolidation. [On Thursday, the Senate voted to limit a farmer's annual subsidy to $275,000, half of the current limit. It is unclear if that cap will survive negotiations with the House, which has voted to keep the current limit, $550,000.]

In Iowa, farmers cultivated land with the help of more federal subsidies than farmers in any other state — $6.75 billion in five years. In a state with no national parks or forests, which keep the land in its natural state, the Iowa countryside has been awash in fertilizers, pesticides, herbicides and animal wastes, some politicians, scientists and environmental groups say.

"We have the most subsidies and the lowest amount of public lands of any state in the union," said Senator Tom Harkin, the Iowa Democrat who is chairman of the Agriculture Committee.

In the last six years there have been 152 fish kills in Iowa — leaving 5.7 million fish floating dead in rivers and lakes polluted by fertilizer runoff or leakage from hog and cattle manure lagoons.

Half of Iowa's lake beaches were temporarily closed last year because of agricultural pollution, said Craig A. Cox, executive vice president of the Soil and Water Conservation Society, based in Iowa.

"Over the last 20 years, we've farmed fence row to fence row, encouraged by federal subsidies, and changed the whole landscape of Iowa," Mr. Cox said. "Farmsteads with groves of trees, patches of wetland and well-planted river banks have been eliminated. Without those natural buffers, we've short-circuited the natural filters and ended up with these water problems."

But those who have large farms say it is wrong to blame them for water pollution. John E. Conrad and his three brothers operate a 5,000- acre spread in Rose Hill, Iowa, that received $921,654 in subsidies over five years and is among the top recipients in the state.

When the government started paying farmers to practice conservation, the Conrad brothers planted grass strips along most of their streams. They have resisted building manure lagoons for their 3,000 hogs in confinement pens; instead they recycle the waste on their fields.

"We have everything the smaller farmer has for conservation," Mr. Conrad said. "If our subsidies were limited, we'd go out of business."

The relationship between federal subsidies and the water problems begins with farm payments that encourage big farms to grow bigger, buying out smaller farmers who tend to be better conservationists, said Michael Duffy, an agricultural economist at Iowa State University.

The big farmers then "plant for subsidies, not for the market," Mr. Duffy said, producing some of the best yields of corn in the state's history. A glut in the global market means farmers are paid $2 less than their cost per bushel. But federal subsidies essentially make up the difference. That cheap corn is then bought by large farms, which feed it to animals, leading to profitable business for meat packers.

"The most drastic charts don't begin to show the revolution in agriculture in the last 10 years," Mr. Duffy said. "Sometimes I think the government is wearing blindfolds when it ignores how the farm program is creating the misery out there."

The number of big farms has doubled over the last two decades while middle-size family farms that manage to stay in business have lost half their earnings. The average number of hogs per farm shot up to 1,300 in 2001, from 400 in 1995, creating the huge manure lagoons scattered across Iowa.

At the same time, the state's water quality has declined, although debate continues about who bears the greatest responsibility.

Without taking sides, the Iowa Farm Bureau has created programs to plant trees and grass buffer strips and to monitor water pollution.

For Mr. McMullen, the water manager in Des Moines, about 70 miles east of here, there is little doubt that agriculture and livestock are the source of his city's water problems. Two Iowa State University scientists recently reported how huge hog manure lagoons were seeping into the state's groundwater.

"The water quality this December is the worst we've had in winter," Mr. McMullen said. "And we're expecting the worst spring on record."

For the first time, he and other city water managers are lobbying Congress to put money in the farm bill to clean up water pollution at its source, the fields and livestock pens.

Last summer Agriculture Secretary Ann M. Veneman agreed to give the state an additional $40 million to improve water polluted by excess nitrates.

While farmers may be reluctant to accept responsibility for water pollution, they are eager to be part of the solution. Jon Judson, a farmer and biologist, persuaded his neighbors to plant borders of native big blue stem and switch grasses to filter runoff.

Mr. Judson's mission was financed by wealthy Iowans who built their homes around an artificial lake that was becoming cloudy.

Now, through the fog covering his farm, Mr. Judson can point to nearby fields where every stream is lined with frozen grasses and new bare trees break the monotony of low Iowa sky.

"Once farmers saw the benefits they brought to a neighbor, then it wasn't hard to get them to put conservation into practice on their land," he said.

"They saw what they had forgotten — that it pays to take care of your soil and water."