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In the driest of times, when the desert grasslands of southern Arizona are baked to a grayish brown, you can step into the shade of a green oasis of cottonwoods and willows, where flycatchers, sparrows and hummingbirds glide over flowing water.
More than 350 species of birds rely on this thriving habitat, many of them stopping to feed on their long migrations. The entire ecosystem depends on the San Pedro River. And the river’s base flow is sustained year-round by groundwater, which seeps from the soil and forms a slow-moving stream beneath the trees.
The aquifer that nourishes the San Pedro is the same water source used by tens of thousands of people in surrounding towns. For decades, wells that supply the growing communities have pumped heavily from the aquifer, drawing down the water table.
The river has long inspired passionate defenders who have warned of its fragility. For years, some conservation activists have appealed for limits on groundwater pumping to help the river survive. They’ve grown increasingly concerned as climate change has pushed temperatures higher and contributed to years of severe drought in the Southwest. And they watched with alarm during the past several months as flowing stretches of the river declined to some of their lowest levels on record, in places nearly running dry before the monsoon rains in July sent pulses of water into the channel.
Despite that temporary boost, some people who have been watching the river for years say they fear that without urgent steps to protect the aquifer, growing portions of the river could soon dry up and stop flowing year-round.
“We’re at this point where if we’re not successful in significantly lowering the amount of groundwater pumping, then we’re going to lose the river,” said Robin Silver, an activist and co-founder of the Center for Biological Diversity. “You’re never going to stop all the pumping. But you have to stop enough so that you stop the drawdown.”
Under Arizona law, there are no rules limiting how many wells can be drilled or how much water can be pumped from wells near the river. Hundreds of new wells have been drilled in the watershed as development has expanded, and groundwater levels have declined in many areas.
Silver’s group has gone to court to try to force the federal government to reexamine water use in the area of Fort Huachuca, arguing the Army base is responsible for a significant portion of the pumping that threatens the river and the endangered species that depend on it. The case in U.S. District Court could settle long-running disputes between conservationists and the government about water use linked to the base, and could in turn affect how much groundwater is pumped in the future.
We’re at this point where if we’re not successful in significantly lowering the amount of groundwater pumping, then we’re going to lose the river.
This summer, while awaiting the court decision, Silver and other activists have voiced concerns that the San Pedro’s flowing stretches have receded to extremely low levels and that if nothing is done to scale back water use, the river’s survival is in peril.
One morning in June, Silver parked at a trailhead and headed off through the desert, walking toward a green wall of cottonwoods. In the treetops, the leaves fluttered in the breeze.
Beside the river, deer grazed in the brush. Birds swooped in the trees. Yellow butterflies floated over the water.
“We love this river,” Silver said. “One of the great joys of my life is desert rivers and just walking up and down.”
His shoes sloshed in the water as he walked downstream. The river has been flowing in this basin for ages, he said, explaining how shallow bedrock pushes the water out of the ground in places along its path.
“The river is a reflection of that aquifer,” Silver said. And the year-round flow, he said, is vital for retaining its unique biodiversity.
“Listen to the cacophony of bird sound,” Silver said. The calls of yellow warblers and yellow-breasted chats rang out from the trees.
“For me, it’s about the diversity and the richness. There’s just nothing like it in the U.S.,” Silver said.
Many other flowing stretches of desert rivers have dried up in Arizona as dams, diversions and groundwater pumping have choked them. What’s left of the Gila River disappears into the sand among irrigated farm fields. The Santa Cruz River dried up in Tucson a century ago as wells pulled away water and sent it flowing to farmlands. Much of the Salt River’s flow is held in large dams that supply Phoenix and surrounding cities, leaving its lower stretches largely dry.
“We have one surviving free-flowing river left,” Silver said. “The Santa Cruz River may have been like this 150 years ago. Now there are no other rivers like this, which is why birders come from all over the world.”
Silver once worked as an emergency room doctor in Phoenix but stepped away from that career to focus on environmental activism.
He has immersed himself in a wide range of conservation fights, seeking protections for Mexican spotted owls and suing the government to press for safeguarding the habitat of endangered Mount Graham red squirrels.
For more than three decades, the San Pedro River has also been a central focus. Through campaigns, petitions and lawsuits, Silver and his group have pushed to protect sensitive areas of the watershed from cattle grazing and safeguard the underground water sources that feed the river.
Some of these efforts have been complicated by the fact that the connection between groundwater and flowing streams is essentially unrecognized in Arizona law.
“Our water laws are not based on reality or physics,” Silver said. “They’re based on politics.”
Without protections for the river’s flows in state law, Silver and other activists have instead sought to push federal agencies to ensure the river keeps flowing, fighting to maintain protections for threatened and endangered species, such as the southwestern willow flycatcher, western yellow-billed cuckoo, northern Mexican garter snake and a rare plant called Huachuca water umbel.
Many stretches of the river have declined over the years as pumping has pulled down groundwater levels. Some stretches that once flowed year-round have retreated underground and become dry sand much of the year, running only when rainstorms send torrents of water coursing onto the riverbed.
On a tree trunk, Silver pointed to a mass of vegetation ensnared in the branches more than 6 feet off the ground.
“When it’s flooding, the water is well over our heads,” he said. “The thing about desert rivers is they’re resilient.”
When floods come surging through during the monsoon, the waters renew the riparian vegetation, helping new cottonwoods sprout in curving rows along the riverbanks.
As he walked through ankle-deep water, Silver exclaimed: “These are baby cottonwoods.”
The saplings stood chest-high in a dense patch on the bank.
“The reason these cottonwoods are here is because the groundwater is at the surface. The aquifer is close enough,” Silver said. “Cool. They might make it.”
The cottonwoods have relatively shallow roots and are sustained by groundwater along the river. The trees can survive even on stretches that no longer flow year-round. But if the water table continues to drop, the trees can eventually die when their roots are left high and dry.
“To me, this is among the most beautiful parts of the river,” Silver said.
The canopy of trees cast shadows on the river, which flowed beside reeds. A great blue heron stood quietly, hunting in the shallow water.
While the river attracts many native birds, the water is filled with invasive species, including various nonnative fish and crayfish, which dart away across the muddy bottom as footsteps approach.
Though the flowing water appears entirely natural, Silver noted that Sierra Vista’s wastewater treatment plant is also releasing water and recharging the aquifer a couple of miles upstream from this flowing stretch in the Charleston area. That inflow has created a mound of water underground, which he said is temporarily helping the local level of the aquifer that feeds the river.
In the long run, however, Silver and others are concerned about what hydrologists have identified as a “cone of depression” created by decades of groundwater pumping — a drawn-down portion of the water table that continues to expand toward the river.
In one report, researchers with the U.S. Geological Survey said they found some improvements in the watershed between 2002 and 2012, including the retirement of wells that previously irrigated farmland and the use of treated wastewater to replenish groundwater.
But the researchers said even with these positive steps, “groundwater levels across much of the subwatershed are declining” because of the pumping for the more than 80,000 residents, plus the effects of pumping years ago. The “cone of depression” between Sierra Vista and Fort Huachuca has continued to deepen, they said, and stream gages at Palominas, Charleston and Tombstone show the river’s base flow has decreased.
Silver said in the long run, even with the inflows from the wastewater treatment plant, the gains could eventually be overtaken by the gradually advancing drawdown of the aquifer.
“If this area goes dry, it means that the full, big cone of depression is claiming it,” Silver said. “Then it’s over. It’s just going to claim everything, including the river.”
The trees swayed in the breeze. High above the treetops, two gray hawks circled and rose in the air currents.
As he walked on, Silver pointed to a vermilion flycatcher, which swooped between branches.
“Hey, buddy,” he said to the bird as it perched on a plant. “It’s hunting.”
For birds in this hot, dry landscape, he said, the shady “ribbon of green” provides everything they need.
“These places, I love them. They’re my life. They sustain me,” Silver said. “And I’m doing what I can to make sure they don’t disappear.”
On the riverbank, Silver pointed out a yellow caution sign. It read: “FORMER MILITARY TRAINING AREA; UNEXPLODED MUNITIONS MAY BE FOUND.”
Fort Huachuca has shaped the area in various ways over the years, contributing to the growth of surrounding communities. The Army base is among the area’s major water users, and it has for years faced litigation by conservation groups.
In the current lawsuit, the Center for Biological Diversity and two other groups — the Sierra Club and Maricopa Audubon Society — argue that groundwater pumping associated with Fort Huachuca, including pumping on and off the base, threatens the river and endangered species. The groups asked the court to throw out a 2014 biological opinion by the U.S. Fish and Wildlife Service that authorized the base’s operations and water use for another decade.
Lawyers for the federal government have denied the allegations and urged the court to dismiss the case. In a court document filed in March, attorneys for the government said Fort Huachuca “has pursued a rigorous water conservation plan, working over the past three decades to reduce groundwater consumption in the Upper San Pedro River watershed.”
They said these efforts have focused on reducing water demand on the base and in the area, and on helping to replenish the aquifer and acquiring water-saving conservation easements in land deals on nearby properties. Federal agencies have studied the expected impacts on the river’s base flow, they wrote, using a model simulation and an accounting of water use and conservation savings.
“Annual pumping from Fort Huachuca’s production wells decreased by over 65% from 1993 to 2012,” the government lawyers said in their motion.
They said the Army has spent over $38 million to purchase conservation easements on nearby properties and implement projects to reuse water and recharge groundwater. These efforts, the lawyers said, have resulted in the base “changing its net groundwater demand from a deficit to a surplus,” and have “fully mitigated” the base’s water use.
Silver and other activists have vehemently disagreed with those claims.
Their dispute centers partly on how the Army base has carried out land deals on nearby properties with the stated goal of permanently shutting off agricultural wells and preventing future pumping. The idea behind these land deals is that they offset some of the base’s impact on water supplies by eliminating water use elsewhere. The base’s officials have been able to claim “water credits” for retired groundwater pumping, helping to improve their overall water footprint calculations on paper.
The base’s recent land deals are detailed in an April 2020 letter that the Center for Biological Diversity obtained through the lawsuit. In the letter, Col. Chad Rambo told Field Supervisor Jeff Humphrey of the Fish and Wildlife Service that since 2015, Fort Huachuca worked with the Nature Conservancy and the Arizona Land and Water Trust to acquire conservation easements on 12 parcels.
“These conservation easements limit the use and development on 7,182 acres in perpetuity,” Rambo wrote. “The Fort has permanently retired 564.57 acre feet (about 184 million gallons) of water usage which could have occurred on the 12 parcels.”
He requested the Fish and Wildlife Service’s agreement that the base “will receive a water credit” for that amount in its next biological opinion. Humphrey replied that his agency reviewed the matter and agreed with the method of calculating the water savings.
Lawyers representing the three environmental groups have argued in court documents that the Fish and Wildlife Service “arbitrarily credited” the base with “illusory water savings.” They said the base’s officials had claimed credit for one property where agricultural irrigation had already stopped nearly 10 years earlier, and said the wildlife agency had “vastly overstated” the water savings.
Silver said the released documents show other instances of base officials “securing fabricated water mitigation credits,” including retroactively claiming credit for retiring pumping that had already ceased years earlier. He said the list of 12 parcels cited by the fort in the April 2020 letter also included two properties that are located not in the San Pedro watershed but in the adjacent watershed of the Santa Cruz River.
In a brief filed in June, lawyers for the government defended how the water-saving credits were calculated and the conclusions of the 2014 biological opinion, saying the conservation groups had presented “several unsupported theories to challenge the agencies’ determination.”
Angela Camara, a spokesperson for Fort Huachuca, declined to speak about the matter, saying the base’s officials have a policy of not discussing ongoing litigation.
Fort Huachuca has a total population of about 14,500, including full-time military personnel, military students, civilian employees and contractors. According to 2013 government data that included “indirect” and “induced” population, there are about 33,000 people living in the area because of the base.
Silver said groundwater pumping linked to the base continues to be a major contributor to the problem, intercepting water that would otherwise flow to the river.
“You’ll hear them say they have a surplus of water. They’re basically creating this paper water to pretend that everything is OK,” Silver said.
“It looks good on a budget, on a ledger sheet, but it’s meaningless to the river.” he said. “The river is going dry. There is no surplus.”
He said the base’s initiatives, like the releases of treated wastewater, don’t change the fact more water continues to be pumped from wells each year than seeps underground to replenish the aquifer.
“It’s a losing battle,” Silver said.
“You can only operate on the negative side of the ledger so long before it catches up with you,” he said. “If you really want to save this river, you’d have to downsize the base, which is obviously really controversial in the community.”
In addition to pushing for a downsizing of Fort Huachuca, Silver and his group have been fighting plans for more development.
They sued to challenge a federal decision to issue a permit for a proposed 28,000-home development near the river. In July, the Army Corps of Engineers announced it had suspended that permit for dredge-and-fill work, a step that appears to create a new obstacle for the project.
Silver praised that decision, but he still sees more threats to the San Pedro.
Driving through Sierra Vista, he passed a golf course that relies on groundwater pumping.
“It’s insane. We’re trying to save a natural treasure and they’re irrigating this golf course with groundwater,” he said.
Elsewhere, he pointed out a construction site where a truck was spraying water, and other newly built houses dotting the dry grasslands on the outskirts of town.
“All those homes that we just passed, they’re sucking out more,” he said.
Portions of the San Pedro River continue to flow year-round at a time when many intermittent streams have been declining throughout the West and the United States.
New research has shown many streams that flow part of the time have become drier across the country, with longer no-flow periods over the past four decades. The study, published in July in the journal Environmental Research Letters, examined data from 540 gages on intermittent and ephemeral streams, and found half of the streams had a significant change in “no-flow duration, no-flow timing, and/or dry-down period” since the 1980s. Some of those streams now dry up for as many as 100 days longer each year.
The San Pedro stretches approximately 174 miles from its headwaters in Mexico to its end in Winkelman, where it joins the Gila River.
About 40 miles of the river between the border and St. David run through the San Pedro Riparian National Conservation Area, which was established by Congress in 1988 and includes intact stretches that flow through lush forests.
Every June, volunteers fan out along the river for a survey to map the river’s wet and dry portions during what is typically the driest time of year. The “wet/dry mapping” effort is organized by the Nature Conservancy and also involves the federal Bureau of Land Management, which manages the conservation area.
On a June day earlier this year, Dave Murray, a hydrologist with the agency, and Rachel Feagley, an intern, met shortly after dawn beside a bridge and drove north on an old railroad grade to their starting point.
Carrying a GPS device and a clipboard, they jotted down coordinates at key points along the riverbed. At first, they found a wide pool, then a dry stretch. They logged any wet section that was longer than 30 feet.
“I think we’re short here,” Murray said, sizing up a puddle on the side of the riverbed. “But this is a start.”
They walked on, shoes crunching in the sand and pebbles. Then, as they came to flowing water, their shoes pressed into soft mud.
After logging some short wet stretches, they trudged on dry riverbed for about an hour, then continued beside flowing water for over half an hour.
Next to a pond, a javelina appeared. It froze and stared, then scampered off.
Murray and Feagley passed ponds where butterflies and moths circled in clouds.
They walked for 5 miles. As they neared the bridge on the riverbed, Murray said the stretch looked wetter than he had expected given how extremely hot and dry the past several months had been.
As for the future, Murray said, the river faces a “double whammy” with the effects of drought and climate change alongside groundwater pumping.
“I try to remain optimistic about it, but it’s got lots of factors against it,” Murray said.
Feagley said she had also expected this part of the river would be drier.
“I’m glad to know that there’s as much water as we found,” Feagley said. “Looking at trends, it’s kind of scary to think what 10 years down the line is going to look like.”
The surveys have been carried out annually since 1999.
The results of the latest mapping are due to be released later this year. In 2020, of more than 120 miles surveyed along the San Pedro’s mainstem, 45.7 miles were wet, representing 38%.
“In general, conditions looked drier this year,” said Holly Richter, the Nature Conservancy’s director of Arizona water projects. She said she expects the combination of many months with extreme heat and no rain will show on the map once the results are completed.
In addition to surveying the San Pedro itself, volunteers also fanned out along its tributaries, including Aravaipa Creek and the Babocomari River.
Many of the survey teams this year saw animals, or signs of them, in areas where water remained, Richter said. Some people spotted black bears.
“During a really super dry year, these habitats are especially important,” Richter said. “Large mammals, including bear and a lot of other species, are really drawn to the remaining pockets of water when it becomes most critical.”
Over the past two decades, Richter said, the surveys have shown that many reaches of the river are stable, while some are declining.
The one area where there has been a significant increase in the stretches with water has been just north of Highway 92, Richter said. In that area, pumping for agricultural irrigation stopped in 2004 and the Army later provided funding for a conservation easement on the property.
Richter pointed out that measurements from a monitoring well near the property, called the Three Canyons conservation site, have shown a long-term rise in groundwater levels.
Despite the improvement in that one area, much remains to be done on a river-wide basis, Richter said, and it’s important “that we minimize our water use to the extent that’s practical.”
Richter has also worked on projects that involve capturing stormwater during rains to boost aquifer levels in places near the river. She said more investments will be needed for projects that help replenish groundwater, both with runoff and treated wastewater.
Richter said she and the Nature Conservancy have worked with Fort Huachuca on conservation easements to help reduce pumping and preclude future water use.
“They’ve been one of our very best partners,” Richter said. “From my perspective, Fort Huachuca has made a very real difference in our water future here.”
Sandy Anderson lives next to San Pedro River, where she runs the Gray Hawk Nature Center. At times when the river floods, she has paddled a kayak on the swollen river for fun. She has also seen the raging waters topple trees.
But as she walked toward the river through sun-singed brush one afternoon in June, she said she had never seen the grassland this parched.
“Look at the mesquite trees. They’re so stressed out, they’re not even flowering this year,” Anderson said. “The river flow has been really low.”
The tall cottonwoods formed a shady corridor that resembled a cathedral. Through the air sailed a great horned owl, and Anderson followed for a closer look.
“This is like a microcosm of what a healthy riparian ecosystem should look like,” Anderson said, heading upstream beside the flowing river.
“Desert rivers are absolutely lifelines for most wildlife, and in a dry year like this, they become absolutely critical,” she said. “Without this, there would literally be a lot of hungry wildlife out there.”
Anderson grew up next to the Colorado River north of Blythe, California, where her father leveled farmland in the Palo Verde Valley. When she first saw the property by the San Pedro in 1984, she was searching for a healthy undammed river, and she knew this was the place.
As she walked on, a row of towering trees loomed ahead on the riverbank.
“When I first walked down here in 1984, I was taller than these cottonwoods,” she said. “I looked right over the top of these trees.”
Now the trees look to be about 70 feet tall.
Looking up at the spreading branches, Anderson said it’s gratifying to see how the ecosystem has flourished over the past few decades. But that doesn’t change the fact, she said, that the flowing, functioning stretches of river that remain are threatened.
“It’s been going down, down. And we are losing the base flow,” Anderson said.
“The base flow is what this is completely and utterly dependent upon,” she said. “That’s why the base flow is so worth fighting for.”
Later, Anderson sat outside in the fading light talking with Silver and Tricia Gerrodette.
Gerrodette lives in Sierra Vista and has been advocating for the river since she moved to the area from San Diego in 1995.
“If we stopped all outdoor watering tomorrow, we would be close to balancing the water budget,” Gerrodette said. “There are things that could be done.”
Gerrodette has closely tracked water use in the watershed, collecting information on the amounts pumped by different cities and utilities to estimate the water deficit.
She said she had been checking the stream gage measurements at the Charleston station on the U.S. Geological Survey website. The data showed the flow in the past few days had been less than 1 cubic foot per second.
“It’s shocking,” Gerrodette said. This stream gage had once before dropped to zero in 2005, Gerrodette said, and the flow again seemed headed toward that mark.
“The river is dying,” Gerrodette said. “It’s dead in places.”
The discussion turned to the long-term threat of the cone of depression in the aquifer, which studies have shown is continuing to expand.
Gerrodette said one way to visualize this is to think of a milkshake.
“If you sink a straw in the middle of the milkshake and sucked up hard, you create a cone of depression. You’ve seen that,” Gerrodette said. “And then when you quit sucking out on the straw, it flattens out, but it flattens out at a lower level than it was before you started sucking.”
With those long-term effects still creeping outward, Silver said, it’s vital to reduce groundwater pumping now.
“The cone of depression is eventually going to hit the river, no matter what. The question is going to be, how deep is the cone and how long will it take to level out? And will you be able to fill the hole?” Silver said.
Along with limiting pumping, he said, there need to be greater efforts to boost recharge into the aquifer from rains, as well as the winter snows that occasionally fall on the surrounding mountains, to “really replenish some of the hole.”
Gerrodette said she’s waiting for the court ruling in the Fort Huachuca lawsuit and hopes the judge will order the base to halt “this bizarre accounting for water.” Overall, she said, the base has done a good job of cutting its own water use, and she’d like to see the city and county governments take much stronger steps to do the same.
When she talks to people about the river, Gerrodette said she’ll often describe the San Pedro as “a miracle of life” that needs to be sustained and protected.
“It’s not dissimilar from climate change in my mind,” she said. “People react when the emergency has actually slapped them in the face, rather than seeing it coming.”
In mid-June, the Charleston stream gage showed the flow dropped very close to zero.
When the monsoon rains arrived in July, the river rose again.
But Ben Lomeli, a hydrologist who previously worked for the Bureau of Land Management, said the summer rains don’t change the long-term picture. Climate change, severe drought and groundwater pumping, he said, are all contributing to shrinking flows in the river.
“The trend is definitely a downward trend for base flows,” Lomeli said.
Silver said despite the fleeting blip of water, the San Pedro is still very much in trouble.
“The monsoons are just providing some temporary flooding,” he said, “but they’re not going to make up the deficit in the aquifer, which is killing the river.”
Follow Ian James on Twitter at @ByIanJames.
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Environmental coverage on azcentral.com and in The Arizona Republic is supported by a grant from the Nina Mason Pulliam Charitable Trust. Follow The Republic environmental reporting team at environment.azcentral.com and @azcenvironment on Facebook, Twitter and Instagram.
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