Photo:  With long delays at the Mexican border, a vendor finds a large and captive market for his pastries.

EL PASO — United States border agents have stepped up scrutiny of Americans returning home from Mexico, slowing commerce and creating delays at border crossings not seen since the months after the Sept. 11 attacks.

The increased enforcement is in part a dress rehearsal for new rules, scheduled to take effect in January, that will require Americans to show a passport or other proof of citizenship to enter the United States. The requirements were approved by Congress as part of antiterrorism legislation in 2004.

Border officials said agents along the southern border were asking more returning United States citizens to show a photo identity document. At the same time, agents are increasing the frequency of what they call queries, where they check a traveler’s information against law enforcement, immigration and antiterror databases.

The new policy is a big shift after decades when Americans arrived at land border crossings, declared they were citizens and were waved on through. Since the authorities began ramping up enforcement in August, wait times at border stations in Texas have often stretched to two hours or more, discouraging visitors and shoppers and upsetting local business.

The delays could remain a fact of life across the southern border for the next few years, border officials said, at least until new security technology and expanded entry stations are installed and until Americans get used to being checked and questioned like foreigners. Last year 234 million travelers entered the United States through land border crossings from Mexico.

W. Ralph Basham, the commissioner of Customs and Border Protection, the agency that manages the borders, said longer waits had resulted from added security measures at border stations that in many cases were aging, outmoded and facing surging traffic. Saying the new document checks were a “security imperative,” Mr. Basham called on border cities, which own many of the crossing bridges, to invest in expanding the entry points.

In the meantime, Mr. Basham said, “A safer border is well worth the wait.”

Wait times of up to three hours have also been reported over the past few months at crossings from eastern Canada. Senator Bernard Sanders, independent of Vermont, who held a series of town meetings with border officials about the lines, said low staffing at border stations was the primary cause there.

The longer lines along the Mexico border have been especially unsettling here in El Paso, a humming border city long comfortable in its marriage to Ciudad Juárez, the bigger and rowdier Mexican metropolis on the other bank of the Rio Grande. Lines of cars and pedestrians at sunrise on the four border bridges here are a routine for tens of thousands of people, including many United States citizens, coming from Mexico on their way to school, work and shopping.

“International bridge wait times continue to escalate, causing frustration and concern in my district and across the nation,” wrote El Paso’s congressman, Representative Silvestre Reyes, a Democrat, in a letter this month to the House Committee on Homeland Security in which he called for a hearing on the matter.

One crosser who said she had struggled with the lines was Wilda Laboy, a 37-year-old American citizen who works in Juárez but is studying for her high school equivalency in El Paso.

“I arrive late, and they don’t let me in,” said Ms. Laboy as she waited to be checked through the Paso del Norte bridge crossing here. “I miss classes.”

Many families that straddle the border are feeling the strain. Border trade groups say the long lines caught them by surprise and are disrupting economic ties vital to both sides of the border.

“We are Americans who live at the border, with our economy and livelihood that depend on moving efficiently back and forth,” said Maria Luisa O’Connell, president of the Border Trade Alliance, which represents businesses all along the border with Mexico. “Now suddenly we have measures that make it less efficient but don’t make us any safer.”

Richard Cortez, the mayor of McAllen, another Texas border town that saw long lines this summer, said the waits had slowed some of the 45,000 trailer trucks that passed the border there each month.

“There’s a misconception that border communities care only about ourselves and our own local businesses,” Mr. Cortez said by telephone. “Our border crossings affect trade across the United States.”

Of $332 billion in trade last year between the United States and Mexico, this country’s third-largest trading partner, more than 80 percent of it moved across the border by truck.

Starting Jan. 31, American citizens returning home by land will have to present either a passport, or a citizenship document like a birth certificate together with a government-issued identity card with a photograph. The requirement is the next phase of the Western Hemisphere Travel Initiative, which Congress adopted in a 2004 bill that enacted recommendations of the commission that examined the Sept. 11 attacks. It is intended to improve antiterror intelligence by gathering a record of everyone entering the United States.

So far the new inspections are not systematic enough to yield measurable results.

The passport requirement has been in effect since January for most citizens returning to the United States by air, and it had a rocky debut because many Americans without passports rushed to apply for one. Passport processing backlogs overwhelmed the State Department, which was forced to relax the requirement during the months of June, July, August and September. That experience has created anxiety among many people who cross at land stations as they anticipate the next phase.

Also in August, border officials said, the Department of Homeland Security issued a directive designed to unify inspection procedures for all the border agencies under its umbrella. It set an eventual goal, with no fixed deadline, for agents to conduct a database query for every person crossing the border.

As a result, queries by agents of both American and foreign border crossers increased. At many older border stations, including El Paso, agents have to enter some queries manually, taking minutes that quickly mount up to hours when thousands of cars and people are waiting in line.

Luis Garcia, the El Paso field director for Customs and Border Protection, said the new policy demanded a change of culture.

“These two communities are very interlinked, not only by trade and commerce, but by family, religion, education,” Mr. Garcia said, standing at the base of the Paso del Norte border bridge as pedestrians streamed by, heading for downtown El Paso. “When a person leaves El Paso to go to Juárez, it’s like going across the street. They don’t consider it leaving the country,” he said.

On an average day, some 21,000 pedestrians cross from Juárez on the Paso del Norte bridge, one of El Paso’s four entryways. Mr. Garcia installed a canopy over the walkway, and water fountains and overhead mist-makers at the checkpoint to cool weary walkers on sweltering days.

As the lines into El Paso swelled in mid-August, Mr. Garcia said, he issued a memorandum directing his agents to gauge vehicle lines in deciding how many travelers to query. If lines were over an hour, agents should run a query only for the driver, unless something about the vehicle aroused their suspicions.

But Mr. Garcia said he did not have great flexibility to speed the lines. “One thing I can tell you up front, as director in El Paso, I will not compromise security for facilitation,” he said.

Border groups say they support tougher security measures but want the border authorities to back them up with increased staff levels and technology to avoid slowing commerce.

Funds for the Border Patrol, which scouts the border between entry points for illegal immigrants, increased by 70 percent since 2005 to $3 billion. By contrast, financing for border station agents, who processed nearly 300 million travelers entering the country legally by land last year, rose by 30 percent since 2005, to $2.1 billion.