By Bob Ortega, CNN Investigates

(CNN) -- From his small mountain town in the Ecuadorian Andes, Darwin Cabrera made the long, dangerous journey through Central America and Mexico and finally across the Rio Grande, into the United States.

But on June 3, 2014, just after he crossed illegally into El Paso, Texas, Border Patrol agents spotted him with other crossers on Sixth Street. As they gave chase, the 18-year-old dove into one of the canals flanking the US side of the river. He didn't surface.

Two days later, Border Patrol agents in a helicopter spotted his body, floating face down. El Paso police officers fished it out of the canal. The local medical examiner recorded the details of the death.

But even though Border Patrol agents saw him go in and saw his body come out, his death did not count in their eyes. The agency's official tally of border-crossing deaths in their El Paso sector that year: Zero. After CNN contacted sector officials with a copy of the El Paso medical examiner's report, they acknowledged the error and said they would add the death to their records.

For 20 years, as part of its mission, the Border Patrol has been tasked with tracking and trying to prevent border-crossing deaths. But an investigation by CNN has found that the agency has been, at best, haphazard about tracking and recording deaths. Despite telling Congress and the General Accounting Office it would provide comprehensive accounting of migrant deaths, it has failed to do so. It has excluded fatalities reported by other law-enforcement agencies, while claiming to include them, and neglected even to count some deaths directly witnessed by Border Patrol agents.

Over the 16 fiscal years ended last September, CNN has identified at least 564 deaths of people crossing illegally in the border region, above and beyond the Border Patrol's tally of 5,984.

Those uncounted deaths were identified through a review of federal, state and local records and databases, and interviews with medical examiners, pathologists, sheriffs and justices of the peace along the border. It is by no means a complete count, and there are strong indications that the actual toll could be thousands higher.

More than half of the uncounted deaths identified by CNN happened in the past four years. Those figures mirror a recent investigation by the Arizona Republic, one of a set of pieces on border conditions that won the 2018 Pulitzer Prize for explanatory reporting. That story documented a significant undercounting of migrant deaths from 2012 to 2016.

The effective erasure within federal statistics of Cabrera's death and so many others has helped minimize the magnitude of the humanitarian crisis associated with illegal crossings. Downplaying the death toll also makes it harder for the United States to assess the full impact of a border policy, in place since the mid-1990s, that uses barriers and other enforcement tools to push migrants to more remote, deadlier crossing points.

That policy was designed to deter crossers, but, as officials realized nearly from the start, its primary impact has been to make the journey far more deadly. Today, experts who study the border fear that deportation and border enforcement strategies being pursued by the Trump admininstration may drive deaths even higher -- making it all the more important to accurately track fatalities.

Carla Provost, the acting chief of the Border Patrol, declined interview requests from CNN. She referred questions to Benjamin Huffman, the Border Patrol's chief of strategic planning and analysis.

Huffman acknowledged that the agency's death tally is incomplete. He said Border Patrol may exclude deaths from local agencies because it doesn't trust their standards. "How other people make these determinations (of what constitutes a migrant death) may not be consistent with what we've done," Huffman said.

But CNN found that the Border Patrol has made little effort to count deaths beyond the ones they encounter. Medical examiners and sheriffs agreed that the Border Patrol doesn't ask for their numbers. And 10 Border Patrol agents and supervisors across the southwestern border and in Washington told CNN that they account only for migrant deaths that Border Patrol agents are directly involved in handling. They don't include other deaths reported by landowners or others to local law enforcement.

"We've only ever counted what we find," said Felipe Jimenez, an agent in the Border Patrol's Tucson sector since 2009. He said that, as an emergency medical technician, he has been involved in many rescues and encounters with deceased migrants.

"The ones we find are our official number. Since I've been in, it's just been what we encounter," said Chris Cabrera, a spokesman for the Border Patrol agents' union who has worked as an agent in the Rio Grande Valley sector since 2001.

Huffman was unable to explain why the Border Patrol's reports to Congress have said it is reaching out to other agencies for death counts when its own agents and supervisors said they are not.

It's impossible to know exactly which deaths are being included in the Border Patrol's count, since their reports offer almost no specific details. The agency said it occasionally adds migrant deaths outside the region it covers. For example, Huffman said they included the well-publicized deaths this past July of 10 migrants trapped in a sweltering tractor-trailer in San Antonio, even though it was Immigrations and Customs Enforcement that responded to the scene. Even with those additions, though, the agency's numbers fall short of CNN's count of known migrant fatalities.

Rep. Henry Cuellar, D-Texas, a member of the House Appropriations Homeland Security subcommittee, said lawmakers rely on correct information to make border policy. "The Border Patrol's mission is to keep us safe, number one," Cuellar told CNN. But, he said, having an accurate picture of where and how many people are dying and being rescued also helps reduce the dangers -- both for border crossers and for the agents who risk their lives to save them.

Cuellar has heard from constituents who are concerned about the death toll. Last year, he said, he added language to the House appropriation bill requiring the Border Patrol to provide greater detail on how it tracks border deaths and what it does to prevent them.

"Folks brought up the issue about 'are we doing enough to have the Border Patrol identify and count deaths along the border,'" said Cuellar. When he added the language, he said, "we thought it was sufficient. ... These are issues I want to bring up and ask them if we should be changing the protocol. We all want to see accurate counts."

'The deaths weren't contemplated'

The surge in crossing deaths began after a 1994 change in the Border Patrol's strategy. That year, the Border Patrol decided to begin building barriers in urban areas such as El Paso, to push border crossers out into more remote and dangerous terrain.

Policymakers believed that once people saw how perilous the new routes were, they'd stop trying, said Doris Meissner, then-commissioner of the Immigration and Naturalization Service, which at the time included the Border Patrol.

But within a year or two, based on how many people agents continued to apprehend, it became obvious that the dangers weren't deterring crossers. And the number of migrants dying on the border had jumped from dozens a year to hundreds. "The deaths weren't contemplated," Meissner said. "Obviously, one can't be anything but regretful about the deaths."

Meissner said the agency had "quite a discussion" about what to do. "But it wasn't, 'Oh dear, we need to change the strategy,' It was, 'Are there things we can do to mitigate what's happening?'"

So in 1998, the Border Patrol launched the Border Safety Initiative, a set of measures to warn migrants about risks, rescue those in trouble, and quantify border-crossing deaths. But the initiative left it up to leaders in each of the Border Patrol's nine Southwest border sectors to decide which bodies to count and how. By the mid-2000s, policymakers on both sides of the aisle were asking questions about the rising death toll. That led Senate Majority Leader Bill Frist, R-Tennessee, to ask the Government Accountability Office to look into what the Border Patrol was doing to track and prevent deaths.

In the 2006 report that followed, the GAO found that the Border Patrol consistently understated the numbers and didn't generally ask local law enforcement agencies, coroner's offices and others for their cases.

"Such incomplete data may in turn affect the Border Patrol's ability to understand the scale of the problem in each sector and affect the agency's ability to make key decisions," the GAO wrote.

In response, Border Patrol officials promised the GAO in 2007 "to establish liaison with local officials to obtain information on those undocumented migrant deaths in which the Border Patrol was not involved." In two reports to Congress, last year and in 2016, the agency reiterated that its count includes border-crossing deaths "whether or not USBP (the Border Patrol) was directly involved." Yet Border Patrol agents who spoke to CNN say that's not their practice.

Lawmakers themselves have faced little political pressure to push for more accurate numbers or to question the deadly strategy too closely. Humanitarian and advocacy groups have called for changes in policies to reduce border deaths. But the thousands of families who have lost loved ones in the desert often feel powerless to complain, because they either live outside the country or include undocumented members who risk deportation themselves. They have not found it easy to unite as a political force.

Even immigrants who are in the country lawfully struggle to bring attention to the disappearances. Take Irma Carrillo Nevarez, a Mexican citizen with legal US residency who lives in Phoenix. Her son Julio and daughter Yadira vanished trying to cross into Arizona through the desert in 1999, she said. She hired a private investigator and reached out to both the Mexican consulate and the Border Patrol. And 16 months ago she provided a DNA sample to the Colibri Center for Human Rights, in Tucson, which helps families to try find and identify relatives who've vanished crossing the border. She says she has gotten little help from the authorities. "We, the poor, we have no money or connections," she said. "We have to speak ... but who do you turn to?"

Confirming border-crossing deaths isn't easy. The flow of migrants and the places that most of them die have shifted over the years, from California in the late 1990s eastward. Arizona became the deadliest crossing point from 2003 through 2013. Since then, it has been the Rio Grande Valley, in Texas.

Other than the Border Patrol, no other federal agency, and none at the state level in California, Arizona, New Mexico, or Texas, seeks to comprehensively track migrant deaths. So gaining a better count involves outreach to scores of local officials and others. And local efforts to track migrant deaths are hit or miss, hampered by poor record-keeping, limited budgets, and the vastness of the desert.

The four border states vary widely in how well local efforts document migrant deaths. But it's the contrast between Texas and Arizona that most clearly shows where the Border Patrol count falls short -- and why.

The agency almost certainly overlooks the most migrant deaths in Texas, which shares a whopping 1,241-mile border with Mexico. But CNN was able to document the Border Patrol's shortfall most clearly in Arizona, where tribal police, county sheriffs, medical examiners and volunteer search groups cooperate to provide a far better tally of remains than their counterparts in Texas. That's why, of the 564 total additional deaths turned up by CNN, nearly three-fourths, 422, were recorded in Arizona.

In Arizona, a clearer gap

In Arizona, local officials and volunteers have ambitiously pieced together their own count of border-crossing deaths, which includes scores of deaths each year not included in the Border Patrol's tally. Their work offers a window into how many more deaths the agency could track if it included data by other organizations.

Leading the effort is the Pima County Office of the Medical Examiner, in Tucson. Staff there doggedly collect suspected migrant death reports from county sheriffs, police and tribal authorities across Arizona's border region, as well as from the Border Patrol.

That collaboration is vital to tracking bodies in the sprawling public lands along Arizona's border with Mexico. Volunteers, meanwhile, help by searching in some of the harshest crossing places, though they often have to wait for permission from federal agencies to work in some of these areas -- for example, in the 517-square-mile Organ Pipe Cactus National Monument, riddled with routes for illegal entry and drug traffickers and once dubbed the country's most dangerous national park.

"There's not too much access, they don't let us go too many places," said Rafael Larraenza Hernandez, founder of a nonprofit volunteer group called Los Angeles Del Desierto, or Desert Angels. But, he said, such searching is vital because "there are too many reports of missing people." The group reports any bodies they find to local law enforcement so they can be recovered and taken to the medical examiners.

Gregory Hess is Pima County's chief medical examiner. His office covers nine other border region counties besides his own -- essentially overlapping the Border Patrol's Tucson sector, or all of Arizona's border region except westernmost Yuma County.

"Border Patrol only finds about 50% of the remains. The rest are found by whoever -- hikers, hunters, ATVers," Hess said.

The Pima County office has been tracking border-crossing deaths and trying to identify remains since 2001. It collaborates with the nonprofit group Humane Borders on a project called the Arizona Open Geographic Information Systems Initiative, which adds data from populous Maricopa County and maps the deaths using GPS coordinates.

That thorough collection of data has allowed Hess to say that in Arizona, at least, the Border Patrol figures for migrant deaths are "a gross underrepresentation." In the last fiscal year, through September 2017, the Border Patrol reported 72 migrant deaths in its Tucson sector. The Pima County Medical Examiner/Humane Borders collaborators, looking at the same area for the same months, counted more than double that number, with 149. Hess's office provides this data each year to the Border Patrol. Despite repeated requests from CNN, neither Huffman nor anyone else at the Border Patrol would explain the discrepancy.

The Border Patrol's undercount in Arizona has been persistent, but growing. More than half of the 422 deaths the agency has not counted over the last 16 years came in the last four years.

Hess said he believes that the Border Patrol somehow changed how it counts deaths starting in 2014, when the gap between their numbers and his widened significantly.

The rising discrepancy does coincide with a change in Border Patrol policy. Huffman, the planning and analysis chief, said that in 2013, the agency stopped running its Border Safety Initiative at the national level, which it had since 2007. The agency left it to be managed by officials at the sector level -- including any decisions about whether to reach out to local authorities and include their data on deaths. Huffman said he wasn't familiar with the details and couldn't explain why the Border Patrol's count in Arizona fell increasingly short after that change.

Juanita Molina, executive director of Humane Borders, said that the gap between the federal figures and the higher count of the Arizona collaboration means that many policymakers and community leaders are unaware not just of the real death toll, but also of the resources required to track and reduce it. "When I talk to foundations about migrants dying within the boundaries of the United States in these extreme circumstances, people think I'm crazy," she said. "They don't understand that thousands of people are dying."

'Texas is a nightmare'

For the past five years, Texas' Rio Grande Valley has surpassed Arizona as the busiest and deadliest crossing point from the south. The gap CNN was able to document between the Border Patrol's figure for migrant deaths and a larger count is smaller than in Arizona -- 94 deaths over the past 15 years, leaving aside El Paso County deaths that the Border Patrol groups with New Mexico.

But that's because, in the Lone Star state, the deaths of many undocumented border crossers are never counted by anyone. "Texas is a nightmare," when it comes to tracking migrant deaths, said Daniel Martinez, a sociologist at the University of Arizona who studies unauthorized migration.

Some of the reasons are physical. Texas' share of the Mexican border is longer than those of Arizona, New Mexico and California combined. The geography across its border varies from the forbidding canyons of Big Bend to the flat floodplains and thorn scrub of the Rio Grande Valley.

Unlike Arizona, where most of the border region consists of public lands, much of the Texas borderlands are private. That limits access by the Border Patrol, local authorities and volunteer search groups.

"We do have problems getting into a few places, usually due to some disagreement with a landowner," said Chris Cabrera, the Border Patrol agent and union spokesman. "Mostly ranchers are fairly cooperative farther north, and closer to the border we have authority to go in anyway."

The larger obstacle, however, is simply that finding bodies in the desert is difficult. "It's very desolate, very remote," Cabrera said. Many sets of remains, scattered by scavenging animals or swept away in washes, may never be found.

Eddie Canales, director of the South Texas Human Rights Center in Falfurrias, in the Rio Grande Valley, works with the Border Patrol to do rescues, leave water on migrant routes, and search for migrants who may be missing or dead. "I've gotten two calls today about someone missing," he said one recent morning.

Based on the calls he receives, he believes that there are multiple bodies that remain lost in the desert for every one his team finds.

When bodies are recovered, they enter a patchwork, dispersed system that doesn't record them all. Of the 21 Texas counties nearest the border, only four employ their own medical examiners. The medical examiners don't necessarily quantify migrant deaths.

"I've been here 13 years, and I've never seen us keeping those numbers," said Annabel Salazar, chief investigator of El Paso County's Office of the Medical Examiner. She couldn't say, for example, how many of the 24 drownings in her county between 2014 and 2017 were of migrants attempting to cross the Rio Grande or nearby canals. But through a public records request, CNN confirmed that 14 of those drowning deaths were described in investigators' reports as undocumented border crossers.

In other Texas border counties, which include some of the poorest in the nation, local justices of the peace are responsible for identifying remains. They are supposed to send them for an autopsy by a medical examiner if needed. But a survey by CNN suggests that often doesn't happen.

Some justices work only part time; all have limited budgets. Most, besides acting as coroners, also handle small claims, arraignments, warrants, evictions and other duties.

Judge Jim Bob Barrera, in Val Verde County, recently was called out to retrieve a body floating in the Pecos River. "It was an hour drive out, then into the ranch. It's heavy brush out there and hardly any road, and huge boulders, so we had to go slow," he said. "By the time I got home it was almost two in the morning."

Barrera said he sends all unidentified remains for autopsies, and that he keeps copies of all the records. He said he could track migrant deaths if he were asked to do so, but neither the Border Patrol nor anyone else has ever asked him.

CNN spoke with 37 justices of the peace across 22 Texas counties at or near the border. Only five said they keep track of migrant deaths.

Justices in six counties said they don't send in all bodies for autopsies, because of the expense. The autopsies, during which DNA and other identifying information is collected, can help identify whether the remains are from an undocumented migrant.

"We're very aware of the cost, and we really try to keep it as low as we can," said Corinne Stern, the medical examiner for Webb County, which covers 3,375 square miles around the county seat, Laredo. Stern provides autopsy services to 10 other counties, at $1,700 per body. All she charges for skeletal remains is $10 for shipping.

Even so, Stern said she was sure many bodies never get sent in. That squared with what CNN heard from justices in several counties that contract with Stern's office. They described migrant deaths to CNN that they did not report to her, and that were not reflected in her numbers.

'Their need to return is huge'

Those who study border crossers fear that, as deadly as the border has been the past 20 years, it's about to get worse.

Jason De León is an anthropologist at the University of Michigan and was named a 2017 MacArthur Fellow for his work on undocumented migration. He's spent much of the last decade investigating who dies crossing the border, what happens to their bodies, and what can be learned from the personal possessions they leave behind.

He criticizes the Border Patrol for what he calls "a systematic effort to undercount and underreport"-- and for ignoring how border enforcement strategies are causing these deaths.

De León worries about the impact of the border policies proposed by President Trump and the GOP majority in Congress: some form of additional border wall and more aggressive deportations.

In the last year, ICE has ratcheted up its detentions of immigrants who have lived in the United States for years, even if they have no criminal record. In recent months, the Trump administration lifted temporary protected status for more than 425,000 Hondurans, Salvadorans, Haitians, Nicaraguans, Liberians, and Nepalese residents. It has extended the program only for about 7,600 people from Sudan and Syria, with decisions on Somalia and Yemen pending. Temporary protected status gives the right to live and work legally in the United States to people who would face extreme hardship if they were forced to return to countries devastated by natural disasters or armed conflicts. Critics complain the programs, meant to be temporary, have let people live here a decade or more.

Then there are the more than 800,000 Dreamers, brought here as children, who were protected from deportation under the Obama Administration's Deferred Action for Childhood Arrivals program. Three federal courts have forced the Trump administration to continue accepting DACA renewals. On May 2, Texas and six other states filed suit to try to force an end to the program. With no legislative solution in view, recipients remain in legal limbo.

In past decades, De León said, most border crossers have come from lives of hardship that to some degree prepare them for the discomforts and dangers they discover en route.

Now, he said, we're going to see "DACA recipients who've never been to Mexico, don't speak Spanish, already are in danger, have not known any physical hardship, and now they're going to walk six days across the desert, trying to return to the only home they've ever known?"

Jeremy Slack, an assistant professor of geography at University of Texas at El Paso, coauthored a recent study that found immigrants with strong personal ties to the United States, such as the long-term undocumented residents now being targeted for deportation, are the most highly motivated to try to return by crossing the border illegally, even when they know the dangers.

"They're the most at risk because they'll keep trying again and again and again," Slack said. "These people have kids and families here. Their need to return is huge."

Together, their work suggests that deportations of Dreamers, TPS holders and other long-term residents could drive border-crossing deaths still higher. But unless the Border Patrol implements the policy it has advertised to Congress for years, federal figures may not register many of those deaths. Lawmakers will continue to make policy without knowing how many lives are being lost under our current system.

Eddie Canales, of the South Texas Human Rights Center, envisions a busy season of rescues ahead. On the political front, there is no relief in sight. "No one wants to invest the political or social capital in dealing with migrant deaths," he said.

He believes that new barriers will not dissuade those with deep motivation to cross into the United States. He offered a prediction: "That wall, it's not going to make a difference," he said. "And if it does, it's going to create more deaths."

CNN's Majlie de Puy Kamp contributed reporting.

Tomorrow: How America's patchwork system for identifying migrants' remains leaves families in limbo.