Two decades ago, a small-time Michigan shopping-center developer named John Rapanos raised the property-rights banner on high: He filled in more than 50 acres of what his own consultant had told him were wetlands without getting a federal permit first. He was taken to court and found guilty of civil violations of the Clean Water Act; a circuit court later upheld the district court's ruling, which brought with it millions of dollars in fines.

Rapanos appealed to the U.S. Supreme Court, and in 2006, five justices voted to vacate the civil judgment against the developer, and return the case to the lower courts. But the justices split 4-4-1 on the bigger question of what standards should be used for protecting rivers and streams.

Justice Antonin Scalia and three others agreed that washes had to be "relatively permanent" to warrant federal protection. Ephemeral and intermittent streams were out of the running. "By applying the term 'waters of the United States' " -- the Clean Water Act's benchmark for federal control of a wash -- to ephemeral streams, wet meadows, and "dry arroyos in the middle of the desert … the Corps has stretched the term … beyond parody," Scalia wrote. Justice John Paul Stevens and three others supported the existing system.

In a separate opinion that has become the ruling's most commonly cited passage, Justice Anthony Kennedy offered a different guidepost: that a wetland deserves protection if it connects to a tributary that has a "significant nexus" with a navigable waterway. But how do you determine that? "Case by case," replied Kennedy.

That left the Corps and the Environmental Protection Agency with the arduous task of figuring out exactly what a "significant nexus" is. Initially, the agencies showed sympathy for non-perennial streams: An early draft of the guidelines sent to the White House Council on Environmental Quality included a provision that would consider the combined effects of similar tributaries on a navigable stream when deciding whether a stream passes the nexus test. But Virginia Albrecht, an attorney for developers and other industries with a stake in the decision, objected. In a letter to Gregory Schildwachter, the Council's associate director, she argued that the provision was inconsistent with the "case by case" direction. 

Under pressure from the White House, the agencies ultimately withdrew the combined-effect provision, and instead included in its June 2007 guidelines a highly technical seven-page process for determining whether something is a "significant nexus." Developers winced at the prospect of going through the process, which seemed to promise more, not less, red tape. And enviros worried that desert streams would be left high and dry. Lance Wood, assistant counsel for the Corps in Washington, D.C., echoed that concern in an e-mail to Wylie, in which he wrote that the guidelines would make "it hard to assert jurisdiction over any particular ephemeral or not relatively permanent intermittent stream."

But Benjamin Grumbles, EPA's assistant administrator for water, said that the agency simply sought to strike a balance between environmentalists' desire to interpret Kennedy's "significant nexus" test as broadly as possible, and the government's determination to defend its decisions in court.

The waters only got murkier as a result.