SAN ANTONIO DE LOURDES, Mexico — In the dappled shade of mesquite trees by the side of a pale yellow schoolhouse, the children finished a song and waited for the priest’s blessing.

The Rev. Juan Carlos Zesati began with a gentle exhortation, citing Pope Francis. “Water is part of God’s creation,” he said as he traced the connection from God to the earth, to life, to community and ultimately to every individual. “We have to respect that connection.”

But the well in San Antonio de Lourdes, a village in Guanajuato State in central Mexico, went dry years ago. The village itself, depleted by poverty and migration, seems to be drying up, too, and only 29 children are left in the primary school. But a half-hour’s drive away, fertile farms pump water from deep underground to irrigate fields that grow broccoli and lettuce for American supermarkets.

“Your communities are suffering,” Father Zesati told a group of mothers and children before delivering his indictment. It is the farms that “are sucking up the water — but just for themselves.”

Then he turned to face a whitewashed water tank, built by the people of San Antonio de Lourdes to collect rainwater from the school roof, raised his right hand, and blessed it. “This seems small for all the problems there are — but it’s a sign of hope.”

It was the first of a day of such blessings in a hilly arid pocket of central Mexico where farmers wait for rain to bring subsistence crops of corn and beans to life.

When Father Zesati arrived in northern Guanajuato four years ago, he quickly learned that he was at the heart of a water crisis, one that is playing out over much of agricultural Mexico.

“What the pope emphasizes is that those who most suffer from the pressure on the earth and from ecological destruction — the first who suffer its effects are the poor,” Father Zesati said. “They are made poor by those who follow an economic model that throws its costs at them.”

The farms in Guanajuato count as one of the great success stories of that model, codified in the North American Free Trade Agreement, or Nafta. Every day, workers stack crates of fresh produce aboard giant refrigerated trucks that roar straight to the Texas border.

“Nafta is all about high-intensive-labor crops,” said Dylan Terrell, the director of Caminos de Agua, an organization that works with universities in the United States to test water quality in the Guanajuato wells, and designs and pays for cisterns and other methods to collect clean drinking water.

As far back as the 1980s, even before the free trade agreement, the government imposed a ban on most new wells in Guanajuato. But water extraction increased exponentially. What allowed that to happen is “a pretty well-known system of bribes and corruption,” Mr. Terrell said.

Every year, farms bore farther into the aquifer, and scientists warn that as they go deeper they are reaching tainted water deposited between 10,000 and 35,000 years ago.

“Here is the challenge for the authorities,” said Marcos Adrián Ortega Guerrero, a hydrogeologist at the National Autonomous University of Mexico. “It is to administer water that is thousands of years old, water that is contaminated with arsenic and fluoride which is causing great harm and that they have never wanted to acknowledge.”

The signs of tainted water seem apparent. The most visible evidence is the prevalence of dental fluorosis, an illness that blackens teeth. Yet the many complaints of joint pain suggest that some people might have developed a much more severe illness, skeletal fluorosis, which occurs when fluoride accumulates in the bones.

“My husband can’t bear the pain in his feet,” said Guadalupe Mata, 39, a mother of three in Rancho Nuevo, the second village on Father Zesati’s route of cistern blessings. “He gets injections, but the pain just comes back. But he still goes to work in the fields to plant chile.”

Her 16-year-old daughter has been hospitalized for kidney trouble, she said. Buying bottled water is far beyond the family’s means; her husband earns about $33 a week.