Nationwide, problems have rippled across the agency's attempts to enforce the Clean Water Act. Last year, internal EPA watchdog Granta Nakayama found that Rapanos and its fallout had hurt more than 500 pollution-enforcement cases, from July 2006 to December 2007. About half involved oil spills. More than 300 cases were dropped altogether, and defendants in 61 cases used Rapanos to weaken the government's arguments.

The guidelines hampered enforcement by narrowing the definition of a tributary to cover only a single segment of an individual stream -- what's called a "relevant reach," Nakayama wrote in an agency memo. "The concept of relevant reach ignores longstanding scientific ecosystem and watershed protection principles critical to meeting the goals of the Clean Water Act," the memo said.

In January 2008, an official in the EPA's Denver office e-mailed the agency's Washington headquarters, warning that "we have literally hundreds of (oil spill) cases in our 'no further action' file due to the Rapanos decision." In February, an EPA official in San Francisco sent out an e-mail -- titled "R.I.P." -- announcing that his office was giving up on a case in which the Justice Department sought civil penalties for a series of Clean Water Act violations.

"It is time to pull the plug in keeping this case on life support," the e-mail said. "With the march of time largely attributable to the impact on the case by Señor Rapanos and his merry band of Supreme Court justices, we had lost many violations due to the statute of limitations."

A few weeks after the 2006 Supreme Court ruling, a district court judge in Texas tossed out a federal criminal charge against Chevron Pipe Line Co., which had spilled 126,000 gallons of oil into an intermittent stream in West Texas. Since that stream is separated from the nearest navigable waterway by 100 miles of intermittent streams, the judge ruled that the tributary didn't pass the significant nexus test. He accepted Chevron's argument that "it seems self-evident that the Clean Water Act does not apply in the absence of water." In Alabama, a conviction and $5 million fine against a manufacturer for polluting a stream was thrown out on the grounds, once again, that there was no "significant nexus."

In New Mexico, state officials said that the EPA had halted inspections of potential polluters in 20 percent of the state's land area because of Rapanos. These areas, known as closed basins, have streams that do not drain to outside areas, much less into navigable waters. The largest such area is the Tularosa Basin in southern New Mexico, home to the Tularosa River, which provides drinking water for several communities.

The problem is that if the EPA doesn't inspect stormwater discharges caused by construction in the growing area, a variety of contaminants could be carried into the river, says Marcy Leavitt, director of water and waste management for the New Mexico Environment Department.

EPA spokeswoman Tressa Tillman would not comment on the cases, but she acknowledged "that since the Rapanos decision, determinations of jurisdiction have become more complex and resource-intensive."

In March 2008, the Army Corps of Engineers declared the L.A. River non-navigable. While that did not remove the river from Clean Water Act jurisdiction, it made it much more difficult to prove that its tributaries, which drain 871 square miles, have a "significant nexus" with a navigable stream and therefore fall under federal control.

In response, Wylie stepped up her activism a notch. In the spring, she leaked a copy of the non-navigable decision to U.S. Rep. Henry Waxman, D-Calif. Then, in July, she joined the expedition down the L.A. River in order to prove that, at least by kayak, the river is indeed navigable for its entire reach.

In early August, Wylie's boss, Aaron Allen, wrote her a letter, proposing to suspend her for 30 days without pay for sending "an unauthorized and inappropriate e-mail message," and for participating in an "unsafe, unauthorized boating expedition on the Los Angeles River that violated a Corps of Engineers policy that prohibits boating in the area."