In Efforts to Secure US-Mexico Border, Ariz. Native Americans Feel Caught in the Middle Tohono O'odham Nation at ground zero in border drug violence.

SELLS, Ariz., June 27, 2013 -- In Southwest Arizona, where the U.S. and Mexico borders meet, the U.S. Border Patrol has made huge strides in capturing border crossers and seizing drugs from Mexican cartels, but there is one stretch of land along the border that has made life a daily hell for a tribe of Native Americans.

The Tohono O'odham Nation, a Native American reservation about the size of Connecticut, is located in the Sonoran Desert, about 60 miles south of Tucson, Ariz., right on the U.S. border with Mexico.

Here, there is no barbed-wire high fence, but open desert, with only a vehicle barrier meant to stop cars but not people.

It is an area where the U.S. government has the fewest resources and the widest open space to patrol, making it a hot spot for Mexican drug cartels and human smuggling operations.

"Nightline" spent 48 hours with U.S. Border Patrol agents and the Tohono O'odham reservation police force to get a firsthand look at the battle on the border.

"The Tohono O'odham Nation is one of our most problematic areas," Arizona Commander Jeffrey Self of the U.S. Border Patrol told "Nightline". "The narcotics smugglers have moved up into the mountainous area. There is not a lot of access."

While border-crossing apprehensions in Arizona are down 43 percent from two years ago, it is a different, more complicated story on the Tohono O'odham Nation. Drug seizures on the reservation are steadily climbing -- nearly 500,000 pounds of marijuana was seized last year, a number that has nearly doubled since 2010. Recently, Tohono O'odham police seized $1 million worth of marijuana in just one week.

But the Tohono O'odham tribal members are caught in the middle of a war between the Mexican drug cartels coming through their community and the U.S. Border Patrol officers who tribal members say have become more aggressive to stop them.

In the Tohono O'odham Nation is "The San Miguel Gate," an area on the U.S.-Mexico border considered to be sacred by the Tohono O'odham. It is the only place where Native Americans can freely walk across the border, but there, the only thing separating Mexico and the U.S. is a low fence guarded by a lone border patrol agent and a light pole powered by a generator.

Verlon Jose, a Tohono O'odham tribal leader whose family has lived on the reservation for generations, and other members of his tribe talked to "Nightline" at "The San Miguel Gate." Jose acknowledged that the Gate carries a myriad of problems.

"Drugs come through here, migrants come through here," he said. "We see harassment from individuals who are moving contraband north, moving migrants north. Homes broken into, vehicles broken into. It's gotten more aggressive."

Jose's cousin Francine Jose lives in a remote part of the reservation and estimated that her house is broken into about once a month by people crossing the border illegally. There is no cell service inside her house so she can't easily call for help -- according to authorities, the police response time to her house can take up to 45 minutes -- and she said the border crossers who walk across her property know it.

"They are constantly breaking in all the time," Francine Jose said. "There was one just recently where they cooked stuff, about a month ago, slept."

Although the U.S. Border Patrol has increased its presence on the Tohono O'odham reservation, Lt. Michael Ford with the reservation's police force is one of only a few dozen native officers who are responsible for patrolling 4,000 square miles of desert to keep the nearly 30,000 Native Americans on the reservation safe.

The Border Patrol uses the latest night vision technology to monitor people illegally entering the U.S. through tracking thermal energy spots -- a technology so advanced he can spot a rabbit moving in the brush from miles away.

The $18.5 billion spent each year on border security has led to a decrease in the flow of border crossers and an increase in drug seizures -- all of which is the result of more manpower, better technology and constant adjustments to every smuggling technique imaginable.

Securing the border does not come cheap. According to the Migration Policy Institute, a think tank, immigration enforcement costs more than all other criminal federal law enforcement agencies combined.

The U.S. Senate today passed its version of the immigration reform bill, but the fate of the bill's provisions, including additional billions of dollars for border security, remains uncertain since the U.S. House of Representatives has signaled they will be considering their own version of an immigration bill.

"In law enforcement, we're constantly playing catch-up," said Guadalupe Ramirez of U.S. Customs and Border Protection, holding a hollowed out compartment that was made to look like a soda crate. "They will use a compartment until we catch onto it. Once we catch onto it, then the percentage of these compartments that get through drops dramatically, so they change compartments."

But much of the border security inside the Tohono O'odham Nation is done the old fashioned way. It's called "cutting for sign," where trained officers search the ground for footprints, tire marks or unnatural damage to vegetation. Smugglers will often wear camouflage clothing and "carpet shoes," which look like cloth-covered booties, so they don't leave shoe treads in the sand, and they will travel at night when temperatures are cooler.

But the people caught and detained might be the lucky ones. As smugglers and their human cargo make their way across the desolate terrain, often what catches up to them is Mother Nature. Lt. Ford said his force finds, on average, six bodies a week in the desert.

"Once you get out there, you're going to run out of water and you're going to run out of options really quick," he said. "Someone is unfortunate to be out there alone they have no hope of coming back."

The dead are brought to Pima County morgue as nameless casualties. Those who go unclaimed will be buried in unmarked graves. More than 100 bodies were recovered in recent weeks and the heat of summer is just getting started.

As for the Tohono O'odham, tribal members who "Nightline" spoke with said their relationship with the U.S. Border Patrol is complicated, at best.

"Are [U.S. Border Patrol agents] welcome in the nation? I would say yes and no," Verlon Jose said. "We're bringing in people who don't understand our culture, our way of life, therefore there is resentment."

While "Nightline" was out with Border Patrol, agents stopped Art Wilson, a reservation native, for driving under the speed limit. They searched his car, but found nothing and let him continue on.

"This is home [and] it's like somebody coming to your house and enforce[ing]," Wilson said. "There's no sense of freedom, feeling invaded on your own homeland."

The Tohono O'odham continue to struggle to deal with the unintended consequences of the U.S. effort to secure the border with Mexico.

"We are on the same team and we are failing at protecting America," Jose said. "When they say that the border is secure along the U.S.-Mexican border that is not true. They are not secure. If you come to Tohono O'odham they are not secure."

ABC News' Lauren Effron contributed to this report