Plans for the sprawling, Valencia-sized Newhall Ranch community call for filling in too much of the Santa Clara River and its tributaries, the Environmental Protection Agency said.

As part of the development, The Newhall Land and Farming Co. would use dirt to fill in a portion of the river’s floodplain, stabilizing it for construction on the roughly 12,000-acre site.

“That fill can destroy or adversely affect water bodies,” said David Smith, manager of the EPA’s wetlands office in San Francisco.

“The Santa Clara is a very high-priority river. It’s an aquatic resource of national importance.”

While the fill and stream channels proposed for Newhall Ranch are better than mass concrete lining of riverbed, he said, “they are proposing to fill a lot of area, about 80 acres.”

The EPA last month sent a letter to the Army Corps of Engineers detailing its concerns about the project. The letter, dated Aug. 24, was sent to Col. Thomas Magness, district engineer for the Army Corps’ Los Angeles District, and signed by Alexis Strauss, director of the water division for the EPA’s Pacific Southwest office.

The document cites the presence of 12 federally endangered plant and animal species in the Santa Clara River.

Smith lauded Newhall Land and Farming for its overall plan for the 21,000-home Newhall Ranch but said there are still unresolved issues.

“There’s clearly a lot of work left to be done,” he said.

Smith said the EPA is also concerned about a perceived a lack of analyses for alternatives to the proposed infill. Also, he questioned how potential effects of the infill will be lessened.

The Santa Clara River is the last river in Southern California to remain unchanneled by concrete, running some 116 miles from the San Gabriel Mountains west through Ventura County to the Pacific Ocean.

The Newhall Ranch Specific Plan was approved in 2003 by the Los Angeles County Regional Planning Commission, and the environmental impact report was compiled over five years at a cost of millions of dollars.

The Army Corps of Engineers and the state Department of Fish and Game are the lead agencies overseeing the EIR.

Newhall Land and Farming Co. spokeswoman Marlee Lauffer has said the developer expects the Army Corps to make its final decision on the report in early 2010.

If the EIR is approved, Newhall Land can begin obtaining the necessary permits required for construction of Newhall Ranch.

The comment period for the draft EIR closed at the end of August, and the Army Corps is reviewing submitted comments, said Jay Field, spokesman for the corps’ office in Los Angeles.

A final report will be released within the coming months with the Army Corps’ response to public comments.

Newhall Land officials are also reviewing the public comments, Lauffer said.

She said protecting the river was key to the design of Newhall Ranch.

As part of Newhall Ranch’s development, 5,700 acres of high country will be set aside as open space. In addition, 970 acres of the Santa Clara River will be protected, and five areas are set aside for protection of the threatened San Fernando Valley spineflower.

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