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Cities across the country are also changing the way they disinfect drinking water. That's because the traditional disinfectant, chlorine, can put toxic chemicals into the water.

But as NPR's Jon Hamilton reports, newer disinfection techniques are turning out to have problems of their own.

JON HAMILTON: It's been a century since water systems in the U.S. began using chlorine to prevent the spread of diseases like cholera and typhoid. David Sedlak of U.C. Berkeley says for much of that time, people thought chlorination was completely safe.

Professor DAVID SEDLAK (Department of Civil and Environmental Engineering, University of California, Berkeley): It wasn't until about the 1970s that we started to realize that chlorine had some unintended consequences. And one of the biggest unintended consequences of adding chlorine to water was that it reacts with some of the organic matter in the water to produce carcinogenic byproducts.

HAMILTON: They didn't pose a big risk. Still, the Environmental Protection Agency decided water systems could do better. So the EPA came up with new rules that prompted many water systems to start using a related disinfectant called chloramine. Sedlak says it didn't produce the same byproducts chlorine did.

Prof. SEDLAK: But then research that came out after utilities had switched to chloramine started to show that there were a variety of different problems that no one had anticipated.

HAMILTON: For one thing, Sedlak says, chloramine could produce byproducts of its own, called nitrosamines.

Prof. SEDLAK: Nitrosamines are the compounds that people warned you about when they told you you shouldn't be eating those nitrite-cured hot dogs. They're about a thousand times more carcinogenic than the disinfection byproducts that we'd been worried about with regular old chlorine.

HAMILTON: And about 20 percent of people in the U.S. now drink water treated with chloramine. Utilities can take steps to prevent nitrosamines from forming in this water, and many do. But chloramine turns out to have other risks, something people in the District of Columbia learned the hard way.

Mr. MARC EDWARDS (Civil Engineer, Virginia Tech): Washington, D.C., is a good case study in unintended consequences.

HAMILTON: Marc Edwards is a civil engineer at Virginia Tech. In 2004, he began testing water samples he'd from D.C. households for lead.

Mr. EDWARDS: I saw these results that were very perplexing, and they didn't really jive with the other data that the water company and the EPA had given me.

HAMILTON: Over time, it became clear what had happened and why. Washington, D.C., had a lot of lead pipes in its system then. But chlorine had helped keep the lead in those pipes from leaching out. Edwards says Chloramine didn't offer the same protection.

Mr. EDWARDS: So when this well-intentioned switch occurred, suddenly we had just unheard-of levels of lead in the drinking water.

HAMILTON: Just how high didn't become clear until Edwards published a study of lead levels in D.C. children a couple of years ago.

On the other hand, places like San Francisco have switched to chloramine without apparent problems. Edwards says that's a reminder that every water system reacts differently to a change in disinfectants.

Mr. EDWARDS: Our water systems have been assembled over a period of hundreds of years, and we've got all kinds of materials out there. We've got cement, you've got iron. You've got three different types of lead-bearing plumbing. You've got copper. You've got plastic.

HAMILTON: And of course the water itself differs from place to place.

Chloramine isn't the only chlorine alternative to run into trouble. Some systems have tried ozone only to find out that it too can create carcinogenic byproducts. And other systems have tried to purify water without chemicals, using ultraviolet light. David Sedlak says that works fine, but there's a caveat.

Prof. SEDLAK: Once you turn off the light, the disinfection power isn't there anymore. And one of the places where we need disinfecting power is in the pipes that take water from the drinking water treatment plant to our homes. And that's because our pipe systems are leaky.

HAMILTON: Which lets in stuff that could make us sick. Sedlak says there are still good reasons for many water systems to move away from chlorine. But he says the chemistry in each place is so different that any change will likely bring its own problems. Sedlak's analysis of the chlorine dilemma appears in this week's issue of the journal Science.

Jon Hamilton, NPR News.

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