Nevertheless, Wylie and other activists had already been heard. In August, Waxman launched a congressional investigation into the implementation of Rapanos by the Corps and the EPA. The same month, the EPA nudged its way into the L.A. River debate, announcing it, not the Corps, would make the final decision on navigability.

Meanwhile, the agencies' handling of Rapanos has also come under attack from the other side.

At a 2007 Scottsdale workshop on the ruling, sponsored by business groups, it was clear that developers and mining companies found the guidelines difficult and confusing. Corps and EPA officials acknowledged that they had no "cookbook" laying out simple rules for defining a "significant nexus."

Phoenix-area attorney Rob Anderson, who represents many regulated businesses, responded: "We don't know what a significant nexus is. We don't know what a navigable water is. We don't know what a relatively permanent water is. … I think that the downturn in the housing market is the only reason we haven't had a complete train wreck on this."

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Meanwhile, the backlog of Rapanos cases grew nationwide thanks to difficulties in deciding jurisdiction over streams. The U.S. Chamber of Commerce pegged the backlog at 15,000 to 17,000 permits in 2007. Even the environmental group Trout Unlimited was affected -- a restoration project in Idaho was delayed a year while jurisdictional issues were sorted out, says Melinda Kassen, director of the group's Western water project.

In response, last June the Corps gave developers and other project builders the right to "opt in" to the agency's permitting system, by agreeing to go with the pre-Rapanos rules. In the vast majority of cases, developers now are choosing to opt in.

"One of the interesting things that is happening is this -- you can go under the old rules and people are just saying, 'Please, let me go under the old rules.' … We hated the old rules, but now we would just love to go under the old rules," Anderson said at the Scottsdale workshop.

But in an interview late last year, Anderson said that the biggest problem with the Clean Water Act regulations is not the Rapanos case or the guidelines; it's that federal agencies have yet to draw up a formal rule that clearly spells out the limits of federal control over rivers and streams. He said, "I believe it is inevitable that the agencies will run into a lawsuit where the courts will say, 'You guys are wrong.' "

In early December of 2008, the EPA and the Army Corps issued revised guidelines on implementing Rapanos. Largely unchanged from the originals, the guidelines do make it harder to prove a river navigable. Now, the federal government must produce written plans for future commercial use of a river, if the river in question has never known such use.

Wylie left her job under a secret settlement that same month, and the congressional investigation that she helped spark wound down, concluding with a condemnation of what the investigators saw as shoddy enforcement of the Clean Water Act.

That investigation also revealed -- with Arizona's Santa Cruz River as exhibit A -- how Rapanos inadvertently made rivers and streams vulnerable to political pressure. Back in May, the Corps had declared 54 effluent-filled miles of the Santa Cruz navigable. That decision drew on extensive scientific and engineering data from federal agencies, academic studies and historians.

But the decision didn't hold. Virginia Albrecht, a lobbyist for the National Association of Homebuilders (and the same attorney who had earlier pressured the feds over the Rapanos guidelines), and other development interests privately protested it. Shortly thereafter, Assistant Secretary of the Army John P. Woodley Jr. suspended the ruling, according to internal Corps e-mails released by investigators for the House Transportation and Oversight and Investigations committees. Other e-mails showed that Woodley acted over the objections of much of the agency's technical staff.

A lot is at stake in this decision: A huge copper mine is planned in the Santa Cruz drainage, a quarry is on the verge of being developed, 13 Pima County road projects are planned along various Santa Cruz tributaries, and the basin holds some of the fastest-growing communities in the West. And since Arizona has a law that prevents its own water-quality rules from being more stringent than federal ones, Woodley's decision to suspend the Santa Cruz navigability ruling could have put dozens of desert streams at risk.

Just as it had done with the L.A. River, however, the EPA waded into the contentious Santa Cruz waters. And in December, the agency declared the Santa Cruz navigable once again. The L.A. River case is still pending.

This year, the battle over river regulation goes to Congress, which will consider a bill aimed at restoring federal river-protection authority. The Clean Water Restoration Act would remove navigability as a benchmark for deciding if rivers and streams fall under federal control, and replace it with a greatly expanded standard that would include intermittent streams. Environmentalists and developers will duke it out over whether this bill would simply restore the feds' pre-Rapanos authority, or expand it considerably beyond that.

If it does pass, the act may be challenged in court by property-rights groups, who would likely argue that the Constitution's interstate commerce clause doesn't give the government that much power over river management, says Pat Parenteau, a Vermont Law School professor who studies the Clean Water Act. 

And Heather Wylie could be involved in that court case. She's decided to go to law school so that she can fight for the environment in the courtroom. Though currently out of a job, she's happy with the attention her protests drew to the obscure Rapanos case and its consequences. "I didn't want to sit around and rot like my colleagues were doing," she says. "I wanted to get out and make the world a better place."

What about John Rapanos, the guy who started the whole ball rolling? In December, more than 20 years after he ruined a wetland, Rapanos agreed to pay a $150,000 civil penalty; he will also spend an estimated $750,000 to re-create the wetlands he wrecked. He has never admitted doing anything legally wrong. But he sure sent the Clean Water Act into a regulatory abyss.

This article was made possible with support from the Kenney Brothers Foundation.