A tatty blanket hanging over a barbed-wire fence is a tell-tale sign that a group of migrants has recently passed by. It's a mild find: over the past decade, more than 2,000 corpses, often desiccated, with the bones scattered by animals, have been recovered from this area of the Sonoran desert, where daytime temperatures can reach 54C and even the vegetation is painfully hostile.

The true number of deaths may be far higher, says Betzi Younglas, a volunteer with Humane Borders, as she steers her truck loaded with 1,100 litres of water down a rutted track through a forest of huge saguaro cacti. Humane Borders is one of several groups working to reduce the number of migrant deaths. Yet even as the numbers of Mexican – and increasingly Central American – migrants attempting the hazardous crossing appears to have declined, the number who die trying remains troublingly consistent.The crossing to America is simply becoming more dangerous.

According to the Washington Office on Latin America, a human rights group, the number of deaths is the equivalent of five migrants dying every four days. It's a situation, say humanitarian groups, that began with policies under President Bill Clinton to tighten the US-Mexico border, but is exacerbated by inertia in Washington over immigration reform and, at a local level, by new powers to demand immigration papers from anyone suspected of being undocumented.

But nothing, says Younglas, has caused as much danger as the hundreds of miles of border walls that have forced migrants further into the desert, away from historical travel routes that have natural access to water. "When the US began walling off the border cities and erecting a barrier right across Texas, they thought the danger of coming through here would deter the migrants," Younglas says. "But they underestimated their desperation."

She stops to check one of dozens of water-filled barrels the group has stationed across the valley that runs 30 miles south to the border. Water has not been drawn from this tank, marked by a blue flag visible from the rough trails, riverbeds or powerlines migrants often follow, since it was last checked three days ago.

"The two biggest dangers out here are dehydration or, in winter, hypothermia," says Younglas. Besides the danger from rattlers and coral snakes, the desert is full of hardship. "Almost every plant in the desert has thorns, so they're getting scratched up. Often they're just walking around on bloody feet. Plus they're being led fast by their guides, the 'coyotes'. If they're injured and can't keep up, they just get left behind."

And those are the ones, sometimes women with babies, who are found dead and end up with the Pima County medical examiner in Tucson. More than 750 skeletal remains – 68% – are unidentified, as migrants rarely carry ID and there are no dental records for a match. "We see about 50 people who have died by firearms," says Dr Gregory Hess, the county's chief medical examiner. "But the vast majority died from exposure."

But a new project known officially as The Arizona OpenGIS Initiative for Deceased Immigrants – Younglas call it the "death map" – may begin to reduce the deaths and help families of the missing recover the bones of their members. Aided by an anonymous $175,000 grant, the database based on information from the medical examiner, law enforcement agencies and research by Humane Borders took five years to develop. Advocates hope that by improving knowledge of border traffic they can influence policymakers and help humanitarian groups identify where they should target their resources.

The Arizona 'death map'. Photograph: Guardian

Out in the Sonoran desert, Younglas explains, increased border patrols are exacerbating the problem. "People are getting left behind a lot more than they used to. When they see the patrol, they scatter. They'll be lucky to find your coyote again because the first thing the coyotes do is take away anything that might tell you where you are. They want you to be dependent." In conjunction with Grupo Beta, the Mexican government's humanitarian organisation that works to dissuade people from trying to cross, Humane Borders distributes maps of its water stations on the Mexican side of the border. The maps show concentric rings indicating how far into the US, say, you can walk in three days. Often coyotes will tell them Phoenix is a two- or three-day walk, when in reality it would take a week or more. But unless they're in distress and want to be picked up, migrants rarely show themselves. When distress calls are received, the information is often too vague – "we are near a black mountain" – to act on.

The group's good relations with the US Border Patrol agency – law enforcement bodies agree not to use water stations as traps – contributes to the programme's success. Water that it doesn't use in the desert stations gets delivered to the Mexican side where in towns like Sásabe the water from the taps runs black. Humane Borders hopes its water runs and mapping programme will bring clarity to the situation and its attendant suffering.

"Nobody should be dying for trying to make a better life for themselves," says Younglas.

But the plight of the migrants is also politically charged. No More Deaths, one of the outspoken groups working on the issue, claims border security strategies that began with Operation Gatekeeper in 1994 are explicitly designed to push migrants into more dangerous crossing areas. "People are trying to cross rugged mountain passes and going down into canyons where it's much easier for them to get lost," says the group's Geoff Boyce. "People are literally being swallowed by the desert."The issue in Arizona has been more politically charged since the US supreme court upheld SB 1070 – a state provision requiring immigration status checks during law enforcement stops and, it is claimed, pushing undocumented migrants and their families deeper into the shadows.

Two hours north in Phoenix, a campaign to oust Sheriff Joe Arpaio, who was recently found to have violated the rights of Latinos by using racial profiling, failed after it did not get enough signatures. Critics say Arpaio is spreading a neo-segregationist culture of fear across the region; Humane Borders regularly finds its desert water stations have been vandalised and drained by people affiliated with anti-immigrant vigilante groups.

This weekend members of migrant support groups were joining the tenth annual Migrant Trail: We Walk for Life, a 75-mile trek from in Mexico Mexico, to Tucson to express solidarity with migrants and to demand an end to deaths in the desert. Organiser Marisol Flores-Aguirre says the number of migrant deaths is directly attributable to "militarisation" of the border. "We talk about the recovery of human remains, not deaths, because we actually don't know how many people are dying out here," says Flores-Aguirre. The desert is so harsh, she explains, that it can be "a matter of weeks" for a body to go through decomposition to become skeletal remains.

The "death map" of Humane Borders shows nearly half of all recorded deaths are on the Tohono O'odham Nation Indian reservation, a nearly 6,000 square miles expanse of desert and mountain that stretches into Mexico. Most occur about 12 miles – or two days' walk – into the reservation. While tribal leaders permit Border Patrol watchtowers and patrols on reservation land, they will not allow Humane Borders or other groups to set up water stations. It's a complicated issue, people with knowledge with tribal leaders thinking say, and one that touches on deep historical roots.

From the Nation's standpoint, they have Border Patrol agents on their land and, with with increasing use of drones and motion sensors, feel they are caught in the middle. In their thinking, water stations will encourage coyotes to bring more migrants through reservation land. The coyotes, who tend to be controlled by drug-smuggling operations, also lead drug mules; those drugs often end up in poor reservation villages susceptible to both drugs, demands for protection and cash inducements. Still, there is anger at the Tohono O'odham Nation leaders for not doing more.On Thursday, the skeletal remains of five migrants were found on the reservation in an area well known for drug and human trafficking. "Migrants are already going through the reservation, so refusing water stations is putting them in greater peril," says Flores-Aguirre. "It's frustrating and difficult."

Andy Adame, a spokesman for Border Patrol in Arizona, says it shares the goal of the humanitarian groups to reduce migrant deaths. It has established rescue towers across the desert where distressed migrants can signal for help, and there are 50 specially-trained agents to rescue – by helicopter, if necessary – migrants from Tohono O'odham reservation land. While the patrol recognises the Sonoran desert, with few roads or points of access, is the most dangerous crossing – it has rescued more than 600 migrants or "aliens" in the past year – it rejects accusations that border security policy is increasing the number of fatalities. "It can really tragic out there," Adame says."You cannot carry enough water to get through that desert, no matter what the smugglers may tell them." The biggest challenge, Adame says, is access to the border. "Smugglers know that, so were building up in that area. It is a crime to enter the United States illegally but it's not a crime for which you should pay with your life."

Border Patrol organises education programmes to inform would-be migrants on the Mexican side of the dangers. "We try to bring the reality to them. Just one days walk into that desert and it's almost impossible to find your way back." In 2000, Border Patrol apprehended 724,000 migrants entering illegally through the western part of Arizona. At that time there were 36 recorded migrants deaths. Last year the patrol intercepted 28,000 and there were nine deaths. "Our job is to secure the borders, and we believe if we can reduce the flow of immigration into Arizona we can reduce deaths," says Adame.