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AUDIE CORNISH, HOST:

From NPR News, this is ALL THINGS CONSIDERED. I'm Audie Cornish.

ROBERT SIEGEL, HOST:

And I'm Robert Siegel. Across the Midwest this summer, scientists are trying to assess the effects of agriculture on the nation's waterways. Some three dozen scientists are collecting water samples and counting fish eggs in about 100 streams. As Abbie Fentress Swanson reports from Missouri, they're looking for pesticides and nutrients used in farming.

ABBIE FENTRESS SWANSON, BYLINE: Eleven miles northeast of Centralia, Missouri, chemist Dave Alvarez dons waders and a bright reflective life jacket before wading into Goodwater Creek. Plenty of fish live in these murky, slow-moving waters along with snakes, crayfish, mussels and snapping turtles. When the water reaches his waist, Alvarez dips a bottle attached to a long rod into the stream.

DAVID ALVAREZ: So with this bottle here, we're collecting water samples, trying to catch any runoff that's coming down through for the pesticides. I just take this bottle. I dip it in the stream. I do it at equal distances across the creek. That way, I kind of get a mixture, a good representative sample of what's flowing through here.

SWANSON: Alvarez is part of a team that's immersing itself in the ecology of streams from Ohio to Nebraska. It's an effort to understand just how agricultural runoff changes water quality. Years ago, scientists didn't test for much in the water, except for nutrients and heavy metals, but now they're able to measure even the tiniest amounts of mercury, pesticides and livestock hormones.

Diana Papoulias is here checking cages of minnows for eggs.

DIANA PAPOULIAS: We know that some of these chemicals that we're finding in the runoff from the ag fields can affect reproduction and egg production. Whether they are at the concentrations that can do that or not, we don't know yet.

SWANSON: Farm runoff is an even more pressing concern because of the extremely wet spring here. Bob Broz is a water quality specialist at the University of Missouri and says narrow windows of dry weather meant that farmers had to apply pesticides and fertilizer in between storms.

BOB BROZ: Anytime you have these heavier rainfalls during the spring, after a drier period when you could have got something put in the field, you're going to see, in most cases, a large amount of runoff.

SWANSON: And because last year's drought prevented some parched fields from absorbing fertilizers, an extra load of nutrients is flowing into Midwest waterways and will end up in the Gulf of Mexico. U.S. Department of Agriculture soil scientist Bob Lerch says once there, they threaten aquatic life.

BOB LERCH: There's the direct impact on the aquatic ecosystem and then there's the downstream impacts on, say, drinking water, or a reservoir, or a recreational water body.

SWANSON: Agricultural runoff feeds into lakes and rivers that hundreds of towns draw their water from. For example, herbicide runoff from a farm in Centralia, Missouri, might end up in Goodwater Creek, which empties into the Salt River, which then flows into Mark Twain Lake. That lake provides drinking water for 70,000 residents. And water treatment plants spend millions on chemicals to clean up that water.

MARK MCNALLY: That's 900 pounds of powdered activated carbon and that is basically metered into the water.

SWANSON: At the plant he manages in northeast Missouri, Mark McNally points out a massive bag of fine black powder being funneled into untreated water. It's removing atrazine, an herbicide widely applied to cornfields in the spring. This powdered carbon alone costs about $130,000 a year, a bill the plant has to pass onto customers.

MCNALLY: Aunt Agnes, you know, on 3rd Street, has to pay more for her water because we have to recoup our money. I mean, we're not in the business to make money. But we can't go broke.

SWANSON: In Central Iowa rivers, record-high levels of nitrate runoff are making it more difficult to meet the demand for clean drinking water. Des Moines Water Works manager Bill Stowe fears long-term effects.

BILL STOWE: Our concern, obviously, is that once you shake customers' faith in the safety of tap waters, you turn them to other sources like bottled water, which is certainly a competitor. It changes our business model and puts us at risk in the long term as a viable utility for providing drinking water for a half million people.

SWANSON: Back at Goodwater Creek, scientists here say results from the Midwest stream study will trickle in after the fieldwork is complete in August. Over the next several years, they'll replicate the study in other regions to try to learn how farm runoff is affecting water quality across the country. For NPR News, I'm Abbie Fentress Swanson in Columbia, Missouri.

SIEGEL: That story came to us from Harvest Public Media, a public radio reporting project that focuses on agriculture and food production.

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