Heather Wylie was a recent college graduate with an honors degree in environmental chemistry in 2003 when she met a biologist with the Army Corps of Engineers at an Earth Expo conference in Ventura, Calif. Shortly thereafter, she took a job as a project manager for the Corps in Ventura. "I had a good understanding of science, but I didn't understand politics," Wylie remembers. "And I thought, I'd love to work with the Clean Water Act."

She got her chance, not only to work with the act, but to mire herself in politics. In early 2007, a Ventura County developer wanted to fill in a half-acre vernal pool for a parking lot. The pools, once widespread in California but now down to 3 percent of their original number, capture water and play host to endangered fairy shrimp.

Wylie wanted the project delayed and the pool left unharmed when the developer graded the 10-acre site. Although an EPA official agreed with her in writing, her boss, Aaron Allen, disagreed and took her off the case. Later, Wylie tried to show that several polluted creeks were hurting the Ventura County lake into which they fed. Again, the same supervisor butted heads with her, although eventually he came around, she says. (Corps officials have declined to discuss Wylie's case on the grounds that they don't discuss personnel matters.)

But it was the Rapanos guidelines that got Wylie really riled. In July 2008, she wrote an e-mail to about a dozen co-workers, citing an internal EPA report critical of the guidelines. That report had been obtained and leaked by the environmental group Greenpeace.

"(The report's author) says what I have been saying for a year now, that the guidance is not consistent with the Rapanos ruling, science or the intent of the CWA, and is putting our waters at risk," Wylie wrote. "Maybe now we will be rescued from having to implement an illegal piece of 'guidance' soon."

The problem, according to Wylie and environmentalists, is that the guidelines made it much harder for federal enforcement agencies to establish jurisdiction over ephemeral streams, arroyos and the like. Before the ruling, it was presumed that the federal government had jurisdiction over any given stream. Afterwards, jurisdiction had to be proven, first, by determining whether the waters were navigable. Then, the agency had to show how a particular reach of a particular tributary affected the navigable water.

"That's ridiculous," Wylie says. "To show how each little creek affects it is just an act of futility. How do you show how each little creek by little creek is having an effect on the Gila River, 20 miles away?"

The city of Buckeye, Ariz., lies in creosote flats far to the west of downtown Phoenix, but it's well on the way to being gobbled up by the megalopolis. Today, Buckeye has 57,000 residents; demographers believe it could have as many as 1.7 million in 50 years, thanks to a handful of new developments such as Trillium, with its projected 8,700 homes. Trillium's 3,242 acres are drained by a series of small, fingerlike washes that come together and ultimately feed into a section of the Gila River deemed navigable by the Corps.

Before Rapanos, the developer would have had to go through the federal permitting process before disturbing any of the washes. Now, the Corps has claimed jurisdiction over only the largest of the streams. That leaves some large washes unprotected, says Dave Smith, a regulator with EPA's Region 9 -- and those washes can carry a lot of water during storms. Had the guidelines allowed agencies to consider the combined effect of several washes, the decision might have been different. "I think I would call this a disagreement among agencies," Smith says. "What it illustrates is that we are all struggling to apply a difficult legal standard."