A Scottsdale-based developer and his contractor have reached an "unprecedented" settlement with the federal government over claims they violated the Clean Water Act by bulldozing, filling and diverting a 5-mile stretch of the Santa Cruz River and its tributaries, the U.S. Justice Department said Tuesday.

The $1.25 million penalty against George H. Johnson and his associates is one of the largest settlements ever obtained by the Environmental Protection Agency under the section of the Clean Water Act that protects against the unauthorized filling of federally protected waterways, officials said.

The settlement, known as a consent decree, is expected to be finalized by the courts after a 30-day comment period. Johnson and his partners reached a record $12.1 million settlement with the state in a parallel case less than a year ago.

Johnson's representatives declined to comment on the settlement Tuesday other than to say that they would adhere to the terms of the agreement.

The federal complaint, filed in 2004, alleged that Johnson and his companies - Johnson International Inc. and General Hunt Properties Inc. - as well as contractor 3-F Contracting Inc., razed and filled an extensive stretch of the lower Santa Cruz and the Los Robles Wash while clearing land for a development in Pinal County near Red Rock.

They did not obtain the necessary permits from the Army Corps of Engineers and altered the course of the Santa Cruz, said Alexis Strauss, director of the EPA's Water Division for the Pacific Southwest Region.

'Very rich landscape'

The land, prior to those activities, had supported a variety of vegetation, including one of the few extensive mesquite forests in Arizona's Sonoran Desert, the government said.

He said the area was a "very rich landscape with important habitat, beautifully braided streams . . . in such a pristine state."

"And all of a sudden, it looked like a big-box parking lot," Strauss said. "To have it bulldozed in such a way was really a concern."

A spokesman for Johnson declined to comment Tuesday on the state's allegations or the specifics of the settlement.

"It's important to note that George Johnson and any of the entities related to George Johnson have not admitted to liability or fault," said Garry Hays, a spokesman for Johnson International. "We will abide by the terms and conditions of the consent decree."

The Justice Department said Tuesday that the case shows that it is serious about enforcing federal environmental rules.

"A seven-figure penalty in this type of enforcement case is virtually unprecedented," said Ronald J. Tenpas, assistant attorney general for the Justice Department's Environment and Natural Resources Division. "It underscores the Justice Department's commitment to enforce the nation's laws that protect valuable water resources in Arizona and other arid western states and to hold violators of those laws accountable."

Settlement with state

In December, Johnson and his partners agreed to pay more than $12 million to settle a similar case with state officials. The alleged violations in that case involved land razing for the same project.

The state's suit alleged that in 2003 and 2004, Johnson's companies and contractors cleared land on two ranches near Red Rock to make way for the community, which would have included 67,000 homes, a resort, golf courses and businesses.

Along the way, workers bulldozed state-trust land, demolished Hohokam archaeological sites and destroyed saguaros and other native vegetation, the state said. The suit also included claims that Johnson brought in domestic goats that wandered into federal land and infected dozens of bighorn sheep with a disease.

More recently, Johnson has been working to reach an agreement with the Arizona Department of Environmental Quality on how to clean up a polluted wash near Queen Creek.

His company Johnson Utilities, a privately owned utility, recently came to terms with department officials on a disinfection plan for the area. A backup at a wastewater-treatment plant resulted in the release of thousands of gallons of raw sewage. No fines have been levied in that case.