The U.S. Army Corps of Engineers is considering a conservation group’s request to revisit a 9-year-old federal permit authorizing a huge development in Benson.

Such a review could seriously delay or theoretically stop the project, but also potentially satisfy many environmentalists’ concerns about it.

The Tucson Audubon Society seeks reconsideration of the federal permit in part because the Corps approved it over objections from the U.S. Environmental Protection Agency. Some objections were raised less than a month before the permit was approved.

Among EPA’s many concerns raised in three letters was the project’s potential to reduce water flows to and dry up the imperiled San Pedro River. That issue remains a hot topic of debate today.

The Corps said its staff is reviewing and discussing Audubon’s detailed request, which came in a May 19 letter, and hasn’t decided how it will respond.

Another issue Audubon raised is that the development, now planned for about 28,000 homes on 12,000 acres, is nearly 50 percent larger than the project the Corps approved back in 2006.

At stake is a federal Clean Water Act permit that the Corps issued for an earlier version of what’s now known as the Villages at Vigneto Project along Arizona 90 southeast of Tucson.

The Benson City Council approved a preliminary development plan for the current project in mid-April. The project’s Phoenix developer hopes to start construction in early 2016.

In June 2006, the Corps approved a permit for Tucson developer Ernie Graves to discharge material dredged and filled from the development site into 51 acres of washes, all tributaries to the San Pedro.

The permit was for a 20,000-home project then called Whetstone Ranch. That project has since gone belly up and been taken over and renamed by Phoenix developer El Dorado Holdings LLC.

Today, the permit remains valid, Corps official Sallie Diebolt said Thursday in an email to the Star.

The federal agency had high hopes for the Benson project at the time the permit was under consideration, Corps records show.

The Whetstone Ranch project “will support the City of Benson’s goal to emerge as a residential, recreational and retirement destination,” the Corps said in 2004.

“Whetstone Ranch will be an opportunity for the City of Benson to help the neighboring cities in Southern Arizona to provide a housing alternative and to help the local economy,” the Corps wrote about the permit application.

But in its letters, the EPA warned the project could damage water quality and cause “significant and irreversible impairment of aquatic ecosystems on the landscape scale.” It raised concerns about potential impacts on endangered species, and wrote that the Corps hadn’t analyzed the project’s effects on a broad enough scale.

The project would cause the loss of ephemeral streams that run only after storms — important to the broader San Pedro ecosystem, the EPA said in a June 2004 letter.

It called that and other damage “substantial and unacceptable impacts to aquatic resources of national importance.”

“Existing water consumption practices in the basin have reached a point where the drawdown of groundwater exceeds the rate of natural recharge,” the EPA wrote the Corps. “Given the potential for the project to accelerate and exacerbate the problem, it is reasonably foreseeable that the San Pedro River could be ultimately converted from a perennial to an intermittent or ephemeral aquatic system.

“This increasing degradation would be contrary to the goals of the (Clean Water Act) — protecting the physical, chemical and biological integrity of the nation’s waters,” the EPA wrote.

Asked to respond to the EPA’s concerns, the Corps’ Diebolt said Thursday that the agency spelled out its responses in a document when it issued the permit. The Star can obtain that document through a Freedom of Information Act request, said Diebolt, chief of the Arizona branch of the Corps’ regulatory division. As of Friday evening, the Corps hadn’t responded to the FOIA request the Star filed Thursday.

Mike Reinbold, a partner in El Dorado Holdings, didn’t return a phone call or an email from the Star seeking comment on Audubon’s request for a Corps review.

Benson’s officials reacted guardedly to the prospect of a Corps re-evaluation of its permit.

“On the one hand, I think if they take an honest look at it, it’s not a bad thing. But if it’s like certain groups, with the Rosemont Mine, getting government agencies to prevent any progress, doing it based on politics not the science, based on speculation of what might happen in the future, it is scary,” City Counclman Jeff Cook said, referring to the protracted controversy over the proposed copper mine in the Santa Rita Mountains.

While Cook said he too is concerned the project could dry up the river, he’s also concerned that project opponents are asking questions about its effects that can’t be fully answered.

“How can you guarantee us this will not dry up the San Pedro? That question can’t be answered. We can have hundreds of agencies doing studies, for hundreds of years, and it still would not be answered.”

Benson Mayor Toney King said he needs more information about Audubon’s request for a revisit of the permit before reacting.

“It’s something we need to take a look at and get questions answered, and we would have to go from there,” said King, who, like Cook, voted for the Vigneto preliminary plan in April.

Bob Hernbrode, vice president of Tucson Audubon’s governing board, called the Vigento project a wakeup call for those concerned about the San Pedro’s future.

“The cart is way out ahead of the horse in this development,” Hernbrode said in a statement. “The Army Corps and the (U.S.) Fish and Wildlife Service need to rectify this by properly evaluating impacts of this new city in the desert.”

Contact reporter Tony Davis at tdavis@tucson.com or 806-7746. On Twitter: tonydavis987