PHOENIX —Two environmental groups on Friday dropped their lawsuit seeking to force the federal government to determine the impact of Fort Huachuca on the San Pedro River.

The fight, however, appears far from over.

In legal papers filed in federal court here, attorneys representing the Center for Biological Diversity and the Maricopa Audubon Society withdrew their demand that Judge Raner Collins order the Army to produce a “biological opinion” to ensure that its operations — including pumping groundwater — do not destroy critical habit.

Attorney Melanie Kay of Earth Justice, representing the groups, said the report was finally produced as required by prior court orders.

But Robin Silver, a cofounder of the center, said the Army is mistaken if it thinks the study will clear the way for Fort Huachuca to continue operations at the current levels.

He said the study is flawed because it presumes the fort can “mitigate” its effects on the river because Cochise County bought private land near Palominas and kept it out of development.

Silver said the fort is claiming credit for 2,600 acre-feet of water a year — close to 850 million gallons — that would otherwise be pumped.

“It’s fake water,” he said.

“There’s no pumping going on in that land,” Silver continued. “So they can’t use this as part of their water budget because it doesn’t exist.”

And Kay said as long as the fort’s operations continue to affect the river — and, by extension, the endangered species that live there — it is violating the law.

Hanging in the balance are the operations of the fort, which in turn impacts much of the future of Sierra Vista.

Silver said it’s not for his organization to tell the military how to comply with the law. But he said one way to cut water use would be to “downsize” the fort, moving nonessential missions elsewhere.

The legal fight goes back to a 1999 decision by the U.S. Fish and Wildlife Service to designate portions of the river as critical habitat. The area is home to at least two endangered species: the water umbel, a semi-aquatic plant, and the Southwestern willow flycatcher.

At issue is how the operations of the fort and the groundwater pumped reduce water to sustain the river.

A 2002 biological opinion found no adverse effects, a conclusion rejected by a federal judge.

Another opinion issued after the first one was rejected conceded that decreased flows in the river would affect the water umbel. That resulted in promises by the fort to conserve water and a new determination by Fish and Wildlife that there would be no adverse impact on endangered species or destruction of critical habitat.

But in 2011, a different federal judge found the latest biological opinion flawed, as it was “not supported by the record or the best available science.” Judge Wallace Tashima also said the report “fails to articulate a rational connection between the facts found and the conclusion made.”

All that, Tashima ruled, meant the Army violated the law requiring that it ensure ongoing and proposed future operations do not jeopardize the existence or habitat of the two species.

Kay filed the lawsuit earlier this year after the failure of the Army and federal officials to come up with a new biological opinion.

“In the meantime, Fort Huachuca has been pumping groundwater without a valid biological opinion in place since 2007,” she argued.

“This pumping continues to intercept water that would otherwise feed the San Pedro’s flows, contributing to the drying of the river and destruction of riparian habitat.”’

With the new opinion issued, Kay said that ends at least this lawsuit.

Silver stressed that dropping the lawsuit does not mean challengers believe the new opinion complies with what the law requires.

“It’s inadequate,” he said. “We’re going to challenge this one also, but that will be a whole ‘nother lawsuit.”

Silver said it’s not like anywhere near 2,600 acre-feet of water were being used on the property when it was being farmed. And he said there is “no chance” pumping on the now-fallow property could be restarted because that would destroy the river.

What all that means, Silver said, is the fort cannot claim that 2,600 acre -feet as mitigating its impact on the river.

That still leaves the question of a remedy if a judge sides with the two environmental groups. Silver said such a ruling would force some tough decisions by the Army, including what missions should remain.

“The signal corps could be moved somewhere else,” he said, as could the intelligence school.

Silver said it’s likely the only essential mission at the fort that could not be moved is the electronic proving grounds. The testing of computers and electronics requires location in a remote area away from electromagnetic interference.