PHOTO GALLERY: Where the Dead Zone begins

THE DEAD ZONE: PART 1

Agricultural runoff in the Mississippi River that flows into the Gulf of Mexico is suffocating sea life and threatening a once-thriving Louisiana industry.

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KAI RYSSDAL: Sam Eaton took us down to the Gulf of Mexico yesterday. Out on the water where Louisiana shrimpers are fighting what's called the Dead Zone. Fertilizer runoff from the Mississippi River sucks oxygen from the water. Today he heads upstream. To the source of most of that runnoff: the Corn Belt. Farms there are some of the most highly subsidized in the country. And that could be the root of the problem.

From the Marketplace Sustainability Desk, Sam has Part 2 of our story.

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SAM EATON: The Gulf of Mexico isn't the only place that's paying the price for industrial agriculture. Midwest cities like Des Moines, Iowa, tap the same fertilizer-loaded rivers for their drinking water. If the nitrogen content reaches a certain point, cities have to issue what are called "blue baby alerts." That's because nitrogen-rich water can inhibit the blood's ability to carry oxygen to the brain.

To deal with the problem, Des Moines has built the world's largest nitrate-removal system. And Randy Beavers with Des Moines Water Works says it wasn't cheap.

RANDY BEAVERS: Well, this facility was constructed for about $4 million, and then it costs us roughly $3,000 a day to operate it.

He takes me through a warehouse of giant tanks called ion-exchange vessels. They use massive amounts of electricity to de-nitrify up to 10 million gallons of water a day. Beavers says the system is already reaching capacity.

BEAVERS: We're experiencing growth here in the metropolitan Des Moines area. And with that growth, we either have to expand this nitrate-removal facility or look at some alternate ways to reduce nitrogen.

Economists call expenses like these the hidden costs, or externalities, of producing massive amounts of cheap corn. The hills of yellow gold that are transformed into everything from soda pop sweeteners to corn-fed beef for 99-cent hamburgers. Fred Kirschenmann with Iowa State University's Leopold Center for Sustainable Agriculture says there's a reason corn is so abundant. Federal farm policy rewards farmers for the amount of corn they grow, not how they grow it.

FRED KIRSCHENMANN: They're caught in a system which forces them to pay attention to simply producing as much as possible, regardless of the cost.

Kirschenmann says as long as yield is king in places like Iowa and Illinois, the problems with nitrogen run-off aren't going away.

KIRSCHENMANN: Corn is a very heavy feeder of nitrogen. You have to have a lot of nitrogen to maximize your corn yields. And so, generally, what farmers understandably will do is put a little bit more nitrogen on as a kind of insurance to make sure that they don't affect their yield. Because if the yield goes, down they're out of business. It's that simple.

With the US Farm Bill up for renewal next year, many see an opportunity to rethink federal farm policy. Between 1995 and 2002 taxpayers doled out nearly $60 billion in federal subsidies to farms along the Mississippi River basin. Critics ask, instead of paying farmers to degrade the environment, why not pay them to clean it up? It's already being done on a small scale in places like the Raccoon River Watershed in central Iowa.

JIM ANDREW: We're at a location that has two of our farm ponds and one is Chief Shabana Lake and the other is Papoose Lake.

Jim Andrew farms 1,300 acres of corn and soybeans. He's part of a federal pilot project called the Conservation Security Program. It rewards farmers for making environmental improvements to their land like building wetlands to reduce the flow of fertilizer runoff.

ANDREW: The more you hold some of that water back the more the crop uses it and it also uses those nutrients in the crop rather than having it flow downstream.

Andrew has also built a series of terraces to prevent erosion and has converted to no-till farming, which means he never has to plow the soil. All of this has allowed him to reduce his nitrogen use by nearly a quarter. Not only is that better for the environment, it's money in his pocket when you factor in the rising cost of fertilizer.

ANDREW: I'm more interested in the bottom line and that's where a lot of people are perhaps missing the point. We push for that high yield to the point that we throw a lot of money into inputs that you really need to analyze and see if they're returning.

Andrew says government payments made the changes on his farm possible. But there isn't enough cash to go around. A recent study found that in some of the top polluting counties the money paid for crop subsidies was as much as 10,000 times greater than federal dollars spent on conservation. Andrew says most farmers are open to change. It's the politicians in Washington that need convincing.

ANDREW: One of the greatest ways to get the farmers vote is before an election in November you give out an extra payment and guess who we vote for then.

But Andrew says every time he puts fertilizer on his crop he thinks about all the towns and cities drinking the same water downstream and the shrimp fishermen with empty nets. The kicker, he says, is that the program that's helped him help them is likely the first to be cut. Especially with the tight budget facing next year's farm bill.

In Des Moines, Iowa, I'm Sam Eaton for Marketplace.