CIENEGA CREEK NATURAL PRESERVE - The stately cottonwoods still tower 50 feet or higher.

The vermillion flycatchers still flash their reddish breasts as they flit from one bare branch to another.

The mule deer still dart into the brush if they sense a human presence.

But some cottonwoods have toppled or their leaves have turned brown, even in a wet July. The streambed here far southeast of Tucson near Vail, four miles upstream from where Cienega Creek merges with Davidson Canyon, is dry - no fish, no frogs, no ponds, no pools. Nothing but shrubs and grass, cottonwoods and willows that were germinated in a wetter time.

An area this dry in the heart of Pima County's Cienega Creek Natural Preserve used to be an exception.

Now it's the rule.

This preserve is a draw for 170 species of birds - and birders come to watch them.

But now, "the creek is waiting for water to return," says Iris Rodden, a natural resource specialist for the County Natural Resources, Parks and Recreation Division that runs the preserve.

For the second June in a row, about 1.2 miles of creek carried water, down from 9.5 miles in June 1984. Also in June the stream carried about 13 percent of predrought flows, says Mead Mier, a watershed planner who oversees monitoring of Cienega's flows for the regional Pima Association of Governments.

Well levels are down about 7 feet since the worst drought on record started in the late 1990s.

And it's not just happening here. Stream flows are being squeezed around Southeast Arizona: Sabino Canyon, the San Pedro River, the Arivaca Cienega and Creek, Redrock Canyon and Upper Cienega Creek. Farther north, the Colorado River, which furnishes much of Tucson's drinking water via the Central Arizona Project, and the Verde River recorded near record-low flows this summer.

Declining stream flows leave less habitat for fish, birds, frogs and other denizens of riparian areas. Already, some fish and frog numbers have dropped.

And in the long run, people will lose, too. The winter storms that give these creeks reliable flows are part of our drinking water supply, and they're declining.

Today some of these streams are running better than a month ago due to heavy July rains. But while monsoon floods germinate summer plants, winter storms are the key to keeping rivers flowing - they settle more gently into the region's streams and deserts. Monsoon storms pelt the landscape and run off.

Winter rains and mountain snows also provide the deepest, most stable recharge sources for the aquifers underlying streams, says Thomas Meixner, a University of Arizona hydrologist. The Cienega Creek watershed, for one, supplies about 20 percent of the Tucson basin's groundwater recharge, PAG says.

"Less winter rain means less recharge. In fact, I would suspect that the last two winters' rains have resulted in almost no recharge to our groundwater aquifers in Southern Arizona," Meixner says.

If that continues, he says, the region's long-term drinking water supply - the only major alternative in the event of a drought-induced shortage in the Central Arizona Project - is threatened.

Megadrought possible

Dry streambeds this summer are no surprise.

After more than a decade of drought, many streams, like Cienega, have seen less flow for years.

Base river flows keep plants such as cottonwoods alive during the dry summer, says Julie Stromberg, an Arizona State University plant ecologist.

Some scientists fear that creeks like Cienega and Arivaca, near the Altar Valley, could be going the way of the Santa Cruz and Rillito rivers. They dried up during the early- to mid-20th century after groundwater pumping lowered the underlying aquifers.

While groundwater pumping is a suspected cause of low river flows in Cienega and other places today, the drought, perhaps aggravated by climate change, also is a concern, experts say.

Last month, a group of Southwestern climate scientists released a report saying it's not clear if human-caused climate change caused the drought. Several much longer and more severe "megadroughts" occurred between years 100 and 1600.

But the warming weather is aggravating this drought by increasing stream evaporation and raising plants' demand for water, say experts at the University of Arizona's Institute for the Environment.

In the future, many experts have said in peer-reviewed studies, human-caused climate change will mean still drier weather here, or at least continued declines in winter rains. Jonathan Overpeck, head of the UA institute, says research shows a one-in-three chance of a megadrought on the scale of the earlier ones in this region by 2100.

"If we move into a world where there is less precipitation, all else being equal, there is going to be less water available to the rivers. I couldn't say the rivers will be actually dry. (But) the rivers will be more susceptible to drying because you have other uses of that river, namely, peoples' consumptive use," says Zack Guido, an associate scientist at the UA environmental institute.

"Impetuous stream"

A century ago, the Santa Cruz River in and near Tucson looked much like Cienega Creek does today.

While it generally didn't flow year-round, a 1909 report by the Carnegie Institution of Washington, D.C., said its banks were lined with thick stands of willows and cottonwoods.

"For months at a time its bed is empty, but at the period of summer and winter rains it is not infrequently filled with a raging torrent," the Carnegie researcher wrote. "When thus swollen by rain, it is a turbid, impetuous stream, bearing along branches of trees and debris of various kinds to be deposited at different points as the water lowers.

"At these times of flood, its power of erosion is very great, and in a few hours the banks in places are deeply cut away, acres of fertile land being swept into the devouring current."

Another report, published in an ornithological journal back in 1912, described the river's flood-plain mesquites as wonders of their kind.

"There were some whose trunks, at the base, scaled over four feet in diameter," wrote the Condor Journal, a publication of the Cooper Ornithological Society. "The large bases branched a few feet from the ground into several limbs, fifteen or eighteen inches in diameter. The tallest reached a height of sixty-six feet."

Huge stands of mesquites still crowd the land east of Cienega Creek, although they've been broken up by a a continuous process of flooding, erosion and lowering of the stream channel that feeds upon itself.

As county wildlife ecologist Don Carter walks along the creek one recent day, he notes that he first started seeing cottonwoods die there about five years ago. He points out three big trees that are dying, with only about half their leaves green. In some areas, more drought-tolerant ash are starting to replace cottonwoods.

He fears that dead trees could become fuel for a fire, killing off the rest of the mesquites and sterilizing the soil, leading to a future of few or no big trees. But his co-worker Rodden, a natural- resource specialist who accompanied him on this tour, tries to be philosophical about the creek's condition and future.

Most of the natural ecosystem of trees, grasses and soils remains, she says as she walks the dry stream. While there are no fish at this spot on the creek right now - "just one day without water, and there's no place for fish," she says - when waters start running or pooling again in the fall or winter, the fish will return.

It's like natural selection, she says - some trees will be able to handle the drought, some will die off before the drought ends.

Frog's range shrinking

A bit downstream, the creek pops out from underground, revealing one of three remaining habitats in the preserve for lowland leopard frogs.

Dennis Caldwell, a private consulting biologist, peers under rocks, through bits of grass and shrubs and sometimes right in the water, to find baby frogs with yellow stripes running down their sides.

That's down from seven or eight such spots 15 years ago when Caldwell started monitoring frogs for PAG as a volunteer.

Millions of the frogs once lived in the Santa Cruz River Basin. But the leopard frog's range in Arizona has been dramatically reduced by pumping, drought, disease and competition from non-native bullfrogs and fish.

Probably 2,000 tadpoles and/or baby frogs live in this section of creek now, Caldwell says. Most don't reach adulthood because disease kills them in the colder winter weather.

"Each spring I do a count," he says, "and I'm lucky to find four adult frogs here and maybe 20 in the whole creek."

Dry pond

Cienegas - marshy wetlands in the desert - once existed in large numbers in Southern Arizona. But many have been pumped dry or damaged by drought and historic overgrazing. One of the best remaining cienegas lies near Arivaca southwest of Tucson - but it was much drier this summer than it used to be.

In 1869, a visitor to the Arivaca Cienega described it as "a large amount of rich meadow land bordering on a never failing stream," according to a paper published in the 1980s in the scientific journal Desert Plants.

The cattle that once filled the cienega are long gone, kicked out in 1985 to make way for the Buenos Aires National Wildlife Refuge. Today, the refuge promotes the cienega as a bird-watching haven. Signs call the wetlands "wildlife magnets" and cottonwoods along neighboring Arivaca Creek "wildlife apartments."

But the creek, which ran regularly 20 years ago, was dry in mid-July. At the cienega, one of two main channels was dry, as were two ponds. Only four springs run wet there today, compared with seven at one time, says Dan Cohan, a senior refuge biologist.

Mary Kasulaitis, a librarian in Arivaca, says the removal of the cattle has also had an impact on the cienega. Since cattle aren't eating the grasses and shrubs, the plants are growing a lot and sucking down water.

Standing by a dry pond inside the creek, Kasulaitis recalls that as a child, she swam and rode horseback in and around it. Richard Conway remembers seeing it full of water in 2007. Conway, a retired geologist, is keeping an eye on both the creek and cienega's condition.

"You get to a place like this and you are all worried about the world going to hell," Conway says as he surveys the creek. "But these things like drought run in cycles."

Besides the drought, the cottonwood forest is being hurt by a lack of flooding due to the presence of a dam upstream of the cienega at Arivaca Lake. The flooding generates baby cottonwood seedlings, so the lack of floods means the cottonwood stands are slowly aging and dwindling, says Buenos Aires' Cohan.

To compensate, the service is doing some "pole planting" of young cottonwoods and willows, putting them in a hole 2 or 3 feet deep.

"We want to preserve the old growth, cottonwood-willow gallery," Cohan says. "It's a valuable ecosystem for wildlife and a limited resource in the Southwest."

With these types of habitats being damaged around the region, he said, "We don't want to see that happen here."

"Less winter rain means less recharge. In fact, I would suspect that the last two winters' rains have resulted in almost no recharge to our groundwater aquifers in Southern Arizona."

Thomas Meixner, a University of Arizona hydrologist

Declining rivers, streams

A rundown of declining rivers, streams and cienegas:

• Lower Cienega Creek: Lost more than eight miles of wet stream flow from June 1984 to June 2012. At the Marsh Station Road bridge, Cienega's average annual streamflow dropped to 0.39 and 0.32 cubic feet per second in fiscal years 2009-10 and 2010-11 before rebounding in 2011-12 to 0.58 cfs - the fourth lowest in 19 years of records.

• Upper Cienega Creek: Lying in Las Cienegas National Conservation Area, Cienega Creek and three tributaries had 4.83 miles of wet stream, compared with 9.98 miles in June 1990.

• Colorado River: Expected to deliver its third lowest spring-summer runoff since 1964 into Lake Powell at the Utah border.

• Upper San Pedro River: Two studies by the U.S. Geological Survey and one by private consultant Laurel Lacher have documented or simulated declines in river flows over the past century. Lacher's study concluded that since 1902, the river had lost 77 to 100 percent of its base flow - the portion supported entirely by groundwater - in various stretches since 1902. An Arizona Daily Star analysis showed that on the river's Charleston gauge, the river's average daily flows in June dropped from 12 to 20 cubic feet per second in 1904 and 1905 to 1 to 2 cfs in recent years. In June, a Nature Conservancy survey found that 48 percent of nearly 50 river miles were wet.

• Sabino Creek: A Star analysis shows a sharp decline in the average daily flows in June at Sabino Dam since 1993, with 10 of those 19 years having zero June flows. David Lazaroff, an amateur naturalist and the author of several books about the canyon, found that the number of days the river flowed at the dam has dropped sharply since 1933.

• Arivaca Creek: It's dry now and has had declining stream flows for years. The stream flow averaged 0.001 cubic feet per second in 2011. In the early 1990s, Phil Guertin, a University of Arizona hydrology professor and researcher, monitored the stream flow every month for two years for the U.S. Fish and Wildlife Service and found it ran most of the time including June.

• Bingham Cienega: Marshy area in the San Pedro River Valley northeast of Tucson had 23 acres of wetlands in the early 1990s. They have been mostly dry since 2003.

• Verde River: In late June, the river flow through Clarkdale in Yavapai County was the lowest on record since 1964.

• Redrock Canyon: Lying close to Patagonia, the 12-mile-long canyon has about one mile of year-round water today, less than half of what ran 25 years ago.

Sources: Pima Association of Governments, U.S. Geological Survey, U.S. Bureau of Reclamation. National Oceanic and Atmospheric Administration, U.S. Bureau of Land Management, Pima County's Office of Conservation Science, University of Arizona Hydrology Prof. Phil Guertin and retired federal fish biologists Jerome and Sally Steffrud.

Contact reporter Tony Davis at Follow Davis on Twitter@tonydavis987