Cottonwood shoots along the Santa Cruz River near Mission San Xavier stand 2 or 3 feet tall. Some seep willows — members of the sunflower family — are just a little shorter. Cattails jut 3 feet high, next to a pondlike stream. Duckweed floats, its roots dipping ever so slightly underwater.

“This is quite the little ecosystem,” marveled Roy Johnson, 87, a retired riparian ecologist who has been studying and writing about the river since the 1950s.

“This is amazing,” he said, observing the rebirth of the Santa Cruz after a century of decline. “I can die happy.”

The river is carrying year-round flows down a stretch on the Tohono O’odham Nation’s San Xavier District that until recently was dry for more than 70 years except after big rains.

And here, unlike through downtown Tucson, the water is once again coming up from the aquifer naturally — not being added artificially through effluent.

The newfound stream is the ultimate sign of the Tohono O’Odham’s successful struggle over the past few decades to gain back a water supply that was taken from them through groundwater pumping by non-Native Americans.

Native Americans have lived for thousands of years along this river, which was usually running wide with perennial water.

The river is why Mission San Xavier del Bac was built just a mile to the east, when Spanish explorers of more than three centuries ago dreamed of harnessing its power to grow crops and raise livestock.

An aquifer with water dating back nearly 12,000 years, to the Pleistocene Era, fed the Santa Cruz.

A caterpillar on a small stick protruding from shallow water in a channel leading to the Santa Cruz River on the Tohono O’odham Nation. Josh Galemore / Arizona Daily Star

But in the 1900s, it was severely over-pumped as Tucson’s population boomed and as mines thrived nearby.

The river went dry near the mission in about 1945.

Now, however, at least a half-mile stretch of the Santa Cruz there has been documented as flowing for the past year, just west of Interstate 19 and about 6 miles south of Tucson.

The underground water table beneath this stretch has been rising a few feet a year since the early 2000s, in some cases up to 5 to 10 feet annually.

That’s because more and more water users, including the tribe itself, are now irrigating crops and supplying homes with Central Arizona Project water brought by canal from the Colorado River, instead of with pumped groundwater.

This same phenomenon is happening elsewhere across the Tucson basin — throughout central Tucson, near the Rillito River and in some places along the Santa Cruz.

It’s also happening in parts of the Avra Valley, where Tucson Water is recharging CAP water into the aquifer at a far faster pace than it’s pumping it out again for human use.

In many places, the water table is rising enough that experts say it’s possible that urban stretches of the Santa Cruz and Rillito also could someday carry year-round, natural flows again, although that will take a lot longer.

This summer, Tucson began releasing reclaimed water into the Santa Cruz in the downtown area, where it runs at very low levels.

An official with the Tohono O’odham Nation’s San Xavier District noted that the Santa Cruz River is already much more lush than it was when the water was first discovered a year ago. Josh Galemore / Arizona Daily Star/
Tribe rejoices

On the reservation, the newly watered river is a direct result of many forces pushing up the once-depleted groundwater table.

But none of those forces are more poignant to the Tohono O’Odham than the impacts of two water rights lawsuit settlements, approved by Congress 21 years apart, that brought large amounts of CAP water to the district lands and allowed some to seep into the aquifer.

“First of all, we’re very grateful to our creator,” said Austin Nunez, chairman of the San Xavier District, in a recent interview in his office just east of San Xavier Mission.

“The vision of our elders in the 1970s, after we settled the lawsuit ... they envisioned seeing water running again down the river, as one of the uses of that water.

“Our elders wanted to see the riverbanks restored as they once remembered it, full of mesquite and cottonwood and thriving with wildlife.”

The water running downriver naturally “brought tears to our eyes. I don’t think we expected it. At least, I didn’t expect it,” said tribal elder Julie Ramon Pierson.

She is the former, longtime president of a group of San Xavier “allottees” who own individual land parcels in the district.

Pierson, who is 70, has no memory of seeing year-round water in the river, but says her mother did — as did many other tribal elders who shared those recollections with Pierson when the water rights settlements were negotiated years ago.

“My mother told me when she was a young girl, she had to go live with her aunt and uncle on the east side of the river. Her aunt would take her to the mission school west of the river, where she saw a lot of willow trees that tribal members used to make baskets,” Pierson said.

“When we were doing water settlement negotiations, the elders would talk about how it used to be in the river,” Pierson said. “That’s what they wanted future generations to see, if we got the CAP allocations.”

A rich riparian history

The San Xavier Native Americans’ ties to the river go back centuries.

“There is a lot of history with us being farmers. That goes way back,” said Tony Burrell, a district council member and an elder himself at 68. “We have always lived here along the river.”

Archaeological records such as tools and rock art show that there were people living in this area at least 10,000 years ago, Tucson archaeologist Deni Seymour said.

While they’re governed by the Tohono O’Odham tribe, many in San Xavier think of themselves as descendants of the Sobaipuri O’Odham Indians, commonly known as “river people.” The Tohono O’odham are commonly known as “desert people.”

The Sobaipuri inhabited the Santa Cruz River Valley as long ago as the late 1200s or early 1300s, said Seymour, Burrell and San Xavier natural resources official David Tenario.

Father Eusebio Kino of Spain and his expedition saw the irrigated farmland up close in 1699 when they visited and founded the mission.

“The fields and lands for sowing were so extensive and supplied with so many irrigation ditches running along the ground that ... they were sufficient for another city,” like Mexico City, Kino observed, according to the 2014 book, “Requiem for the Santa Cruz.”

A century of decline begins

Crop irrigation continued into the early 20th century, says the book, which Roy Johnson and three others co-authored, telling the definitive story of the river’s decline.

In the early 1900s, the San Xavier area lay next to some of the 9 miles of perennial stretches of the Santa Cruz near Tucson, the book says. The rest were in downtown Tucson.

But in 1931, then-Tucson Mayor C.K. Smith laid out a blueprint for future water development that would ultimately wreck the American Indians’ groundwater supplies.

“We are a growing community. We have an adequate supply for the present but we must look forward to the future,” Smith told a U.S. Senate hearing, as reported in the “Requiem” book. “Eight or nine miles up the river is the Indian Reservation. It is the most available place for water in the entire river course.”

Smith’s proposal to draw from the aquifer beneath the reservation was rejected by Congress, but Tucson later did start pumping heavily south of the city. That helped dry up much of the tribe’s groundwater supply.

Robert Webb, a retired hydrologist, is astonished by the number of cottonwood shoots sprouting up in a channel leading to the Santa Cruz River on the Tohono O’odham Nation. Josh Galemore / Arizona Daily Star
Lawsuit brings back the water

The Tohono O’odham filed a major lawsuit in 1975, charging that pumping by Tucson and neighboring copper mines had deprived the tribe of groundwater to which it possessed valid legal claims.

The ensuing legal settlements gave the tribe and district clear-cut rights to tens of thousands of acre-feet of CAP water.

At San Xavier, much of that water went into the district’s cooperative farm, which adjoins the river to the west. “Return flows” from the farm are a major source of the river’s rebirth.

Some of the 7,000 acre-feet of water that irrigates the farm’s crops each year isn’t consumed by them. The leftover water seeps into a neighboring aquifer that directly feeds the Santa Cruz.

The water table at San Xavier is also rising because the mining company Asarco has for the past decade used up to 9,000 acre-feet of CAP water annually in place of groundwater that it used to pump for its Mission Mine, in neighboring Sahuarita to the south.

Across I-19 east of the reservation, Tucson Water and other uses started replenishing a series of artificial basins at Pima Mine Road with CAP water more than 20 years ago. The basins now recharge around 25,000 acre-feet yearly.

Still more CAP water could be replenishing the Santa Cruz in the future. The U.S. Bureau of Reclamation is now reviewing plans from the San Xavier District to more than double the size of its cooperative farm, to about 2,300 acres. That, in turn, would require using far more CAP water — which would mean more water replenishing the aquifer.

Also, two pipelines are planned to take CAP water to Green Valley and the Farmers Investment Co. pecan groves in Sahuarita. If they are built, that would take more pressure off the aquifer.

A group of scientists, community members and journalists walk through a channel leading to the Santa Cruz River on the Tohono O'odham Nation Wednesday, Sept. 18, 2019. Josh Galemore / Arizona Daily Star
A look at the River

Tony Burrell, the tribal district council member, recently jointed two other district officials and three researchers and water experts, including author Johnson, on a visit to the river.

Normally, the river is closed to the public but the district’s Natural Resources Department allowed the visitors to see what it looks like.

Three new streams have formed inside a riverbed up to 2,000 feet wide in this area. Two run relatively fast; the third runs slowly, creating marshy conditions. All are lined with tree seedlings, shoots and tall grasses.

A district official, Cie’na Schlaefli, noted that the river is already much richer and lusher with vegetation than it was when the water was first discovered a year ago.

In fall 2018, officials brought a drone to the river to take video shots, and “it was all bare, but the water was flowing,” said Schlaefli, a natural resource specialist for the district.

The Santa Cruz at San Xavier was first in line in the Tucson area to recover naturally, because it’s underlain by a thick layer of bedrock fairly close to the ground surface, said Robert Webb, a retired U.S. Geological Survey hydrologist, and Eric Holler, a retired U.S. Bureau of Reclamation engineer who has worked closely with the tribe on river management.

The groundwater here has always been shallow, with a basaltic dike forcing up the water, said Webb, another co-author of “Requiem for the Santa Cruz.”

Holler, who grew up in Nogales in the 1950s and ’60s, recalled riding past the river with his father en route to Tucson when he was about 10, and noticing that mesquites, willows and cottonwoods were dying off.

“I’d ask my dad why, and he said, ‘they were poisoning them, sucking too much water,’” Holler said. “It’s not a swimming pool down there in the aquifer — it’s more like a saturated sponge.”

Today, Johnson and Webb repeatedly used words like “amazing” to describe plants like a 10-foot-tall sunflower, and purple aster blossoms atop tall plants.

Pointing to a gently running stream, Holler noted that the water is clear — “with no smell. It’s got algae, but it’s not overwhelmed by algae.”

A sunflower grows in a channel leading to the Santa Cruz River on the Tohono O'odham Nation Wednesday, Sept. 18, 2019. Josh Galemore / Arizona Daily Star
For the future, some concerns

As for the future, “There’s a whole bunch of irons in the fire right now,” Holler said. “No one can tell me what the ultimate result will be.”

Tucson Water plans to increase pumping pressure in the area, by doubling the amount of groundwater it takes from its Santa Cruz well-field east of the river over the next decade.

The well-field lies directly north of the Pima Mine Road recharge basins and contains CAP water that was sunk into the basins. The pumping increase will significantly reduce flows from the recharge area into the river’s aquifer.

At the same time, not all the impacts of rising water tables will be positive, Holler said.

On the Native American reservation, if water rises too high it could clog up the farm fields. Then, “you’d have to put in a drain system like they do along the Colorado River near Yuma,” where groundwater levels are high, Holler said.

Tribal leaders’ main concern today is that when the water resumed flowing last year, a lot of off-road vehicles started coming in. The vehicles left behind scars of tire tracks — still visible in the riverbed.

Because of concerns about trespassing, the district doesn’t plan to promote this river water as a tourist attraction, Burrell said.

Indeed, tribal leaders such as Nunez declined to talk publicly about the river water for some time, until it became clear that many passersby were aware of it. For now, said Burrell, “it will be left as it is.”

In Tucson, rising water levels in the river could someday leach pollutants out of long-abandoned landfills there into the Santa Cruz, Holler said.

Tucson Water Director Tim Thomure said that’s unlikely, however. The depth of water in the river is unlikely to ever be high enough, he said, adding that one landfill has already been removed and the rest will either be cleaned up or removed over time.

Over the long haul, the biggest unknown is how long all this CAP water will be available to keep replenishing the Santa Cruz.

The Colorado River is expected to shrink over the coming decades because of climate change, although no one can say for sure how much. That would eventually trigger cuts in Tucson’s CAP supply. The Colorado provides 40% of Arizona’s water supply.

But for now, the Santa Cruz near San Xavier is a story about how importing water from a river 300 miles away is restoring another one, long left for dead.

“The vision of our elders in the 1970s ... they envisioned seeing water running again down
the river, as one of the uses of that water. Our elders wanted to see the riverbanks restored as they once remembered it, full of mesquite and cottonwood and thriving with wildlife.” Julie Ramon Pierson, Tribal elder

Contact reporter Tony Davis at tdavis@tucson.com or 806-7746.