Federal officials have suspended a crucial permit for a 28,000-home development planned in Benson.

Critics of the massive project cheered the decision, saying it allows for greater scrutiny of how Villages at Vigneto could affect the San Pedro River and wildlife that depends on it.

In a July 20 letter to the developer, a U.S. Army Corps of Engineers official said the suspension was “in the public interest,” pending interagency consultation about the project’s impact on protected species and their habitats.

“The suspension is effective immediately,” said the letter, which the Star obtained Thursday. “Upon receipt of this correspondence, you are ordered to stop those activities previously authorized by the suspended permit.” The permit, which applies to 8,200 acres of the 12,300-acre development, allowed the developer to fill 51 acres of desert washes in order to build the master-planned community.

Mike Reinbold, development partner at Phoenix-based El Dorado Holdings Inc., said in an emailed statement that he supports the Corps’ effort to comply with environmental regulations.

“We have every expectation that after full consideration of endangered species issues by the Army Corps of Engineers and the U.S. Fish and Wildlife Service that our project will move forward,” he wrote. “We are fully cooperating with the (agencies) as they move through their mandated reviews.”

The move comes just days after Benson’s City Council unanimously approved a final master plan for the Vigneto project, which envisions a golf course, vineyards, schools, lakes, medical facilities, and commercial and office space.

Environmentalists have argued the approval was premature, without resolution to concerns about whether the project’s federal Clean Water Act permit — which the Corps issued in 2006 to an earlier developer — was still valid. The previous developer transferred the permit to El Dorado in 2014.

Critics say newly listed endangered species, and the expanded footprint of the new project, mean the Corps must reconsider the original permit, starting with formal consultation with the U.S. Fish and Wildlife Service.

“This represents an important first step to reassess an outdated and erroneous permit, based upon changed circumstances and new information,” Karen Fogas, executive director of the Tucson Audubon Society, said in an email. The group first called for reevaluation of the permit more than a year ago.

The Corps and wildlife service are working to determine the appropriate scope of consultation, said Steve Spangle, field supervisor for the wildlife service’s Arizona ecological services field office.

Benson City Councilman Chris Moncada said Thursday that he doesn’t think consultation will delay the project, which is expected to break ground next summer.

“I’m disappointed they pulled the permit,” Moncada said. “But I’m convinced that once they do their due diligence, which I honestly have no problem with, they’ll come to the conclusion that this development still can be done with minimal impact.”

The Corps has already agreed to “informal consultation” on a 144-acre parcel to be devoted to mitigating effects of Vigneto’s filling of desert washes, Humphrey said. Informal consultation indicates the agency does not believe there will be impacts, and the wildlife service has 30 days to respond to that assessment.

REQUESTS FOR MORE STUDY

Last year, the U.S. Fish and Wildlife Service asked the Corps to start formal consultation on Vigneto’s potential impacts, a process that could result in the developer having to reapply for the permit.

The service said consultation should evaluate impacts on two federally protected species — the Western yellow-billed cuckoo and Northern Mexican garter snake — which have been listed since the original permit was issued 10 years ago. The service also said that, since Vigneto has a 50 percent bigger footprint than its predecessor, Whetstone Ranch, the Corps should reevaluate the project’s impact on critical habitats for protected species, including the endangered jaguar.

With that request, the service aligned itself with environmental groups that had been calling for the Corps to reevaluate the permit.

When no decision came from the Corps, conservationists took their argument to court. In May, six environmental groups filed a lawsuit against the Corps and wildlife service, arguing that Section 7 of the Endangered Species Act requires federal agencies to consult with the wildlife service before issuing a permit for a private construction project that may affect an endangered species. The service has been dismissed from the suit, since the Corps is the agency responsible for initiating consultation, said Chris Eaton, an attorney with Earthjustice, the firm that filed the suit.

The Corps’ move to suspend the permit doesn’t resolve the lawsuit, but it’s an important step toward consultation, Eaton said.

“The Corps’ good-faith action to put Vigneto’s development on hold while the Corps and (wildlife service) determine what additional environmental reviews and conditions are necessary is good news for the San Pedro River, and the communities and wildlife that rely on it,” Eaton said in an email.

IMPACT OF CONSULTATION

Formal consultation typically takes about four months, but extensions can draw it out for much longer, depending on the complexity of the project and the scope of the analysis.

Consultation could have minimal implications for Vigneto if the Corps limits its evaluation to the direct effects of what the permit explicitly authorizes: using dredge-and-fill materials to fill in desert washes in preparation for construction. That’s all the Corps considered when it issued the original permit in 2006, despite requests from the wildlife service and the Environmental Protection Agency to evaluate impacts to the ecosystem around the San Pedro.

For the wildlife service to be able to demand substantial changes to the development plan itself, the consultation would have to conclude the project jeopardizes the survival of a protected species, said Jeff Humphrey, a spokesman for the service.

Environmental groups suing the Corps want consultation to include six protected species — the jaguar, ocelot, Western yellow-billed cuckoo, Southwestern willow flycatcher, Northern Mexican garter snake and lesser long-nosed bat — and encompass the entire 12,300-acre development, not just the 8,200 acres permitted for the earlier Whetstone project. The developer has said the additional 4,100 acres can be permitted separately.

In addition, the consultation should consider not just the direct effects of the developer filling in desert washes, but also how the project’s groundwater pumping could impact those protected species and their fragile riparian habitat, environmentalists say.

A $1 million U.S. Geological Service study aimed to explore the effects of groundwater pumping, but was defunded in 2010 amid budget cuts. The Tucson-based Center for Biological Diversity — one of the parties in the lawsuit — recently funded a scaled-down version of the USGS study. The new report found that Vigneto’s groundwater pumping could harm the St. David Cienega and infringe on federal water rights established with the creation of the San Pedro Riparian National Conservation Area.

And earlier this month, Arizona State Park and Kartchner Caverns State Park officials demanded further study on how Vigneto could affect the wet cave system that is a major tourism draw for Cochise County.

Fogas, of the Audubon Society, said 95 percent of riparian areas in Arizona have been exhausted, and the San Pedro is one of the few that remain.

The effects of groundwater pumping today might not be seen for decades, she said, “but it’s a road that once you pass down it, it’s really tough to backtrack.”

Contact reporter Emily Bregel at 573-4233 or ebregel@tucson.com. On Twitter: @EmilyBregel