Construction of a 30ft-high section of Donald Trump’s border barrier has begun in the Organ Pipe Cactus national monument in southern Arizona, a federally protected wilderness area and Unesco-recognized international biosphere reserve.

In the face of protests by environmental groups, the wall will traverse the entirety of the southern edge of the monument. It is part of the 175 miles of barrier expansion along the US-Mexico border being funded by the controversial diversion of $3.6bn from military construction projects.

This will include construction in Texas, New Mexico as well as Arizona where, according to a government court filing, some 44 miles of new barrier construction will pass through three federally protected areas. These are the Organ Pipe wilderness, Cabeza Prieta national wildlife refuge and San Pedro Riparian national conservation area, the location of Arizona’s last free-flowing river.

The Trump administration has deemed the new structures necessary due to a “national emergency” of unauthorized immigration into the US. According to CBP, in the 2019 fiscal year there have been 14,265 apprehensions in the Tucson sector, where the Organ Pipe wall is going up, compared to 51,411 in the nearby Yuma sector of Arizona and over 205,000 in the Rio Grande Valley of Texas.

Border wall construction at the Organ Pipe Cactus national monument. Photograph: Center for Biological Diversity

Yet Organ Pipe is a contentious setting. “What is being proposed is bulldozing one of the most biologically diverse regions of the entire United States,” said Amanda Munro of the Southwest Environmental Center. “Walling off these precious places would be a colossal mistake and a national tragedy.”

Organ Pipe, located south-west of Tucson, Arizona, is a 330,000 acre wilderness home to mountain lions, javelinas, the endangered pronghorn and “more bird species than can be listed”, according to the National Park Service website. It is also a deeply significant area for the nearby Tohono O’odham nation which has long opposed Trump’s border wall on their ancestral lands.

“This unneeded, expensive blight will use precious water for its construction, cut off wildlife species from their habitat; and its all-night lights will destroy the clear night skies,” said Kevin Dahl of the National Parks Conservation Association.

Much has changed since the 1970s, when Dahl first visited Organ Pipe as a high school ecology student. At that time the border between the US and Mexico was easily and frequently crossed. “National Park rangers would walk across the border and eat lunch,” said Dahl, motioning to a roadside restaurant in Mexico clearly visible behind the vehicle barriers, reminiscent of the Normandy beaches on D-day, that make up a section of the border.

Donald Trump’s border wall will traverse the entirety of the southern edge of the monument in Arizona. Photograph: Jim Watson/AFP/Getty Images

In the decades since, Dahl has witnessed a dramatic increase in border militarization and barrier construction, including miles of fencing, access roads and a surge of border patrol agents. The new construction will replace pedestrian fences and vehicle barriers, which can easily be traversed by animals, with a 30ft tall bollard wall and accompanying infrastructure. There are fears it will impede migration, cut animals off from water supplies and increase flooding.

“They haven’t thought the design through,” said Dan Millis, the Borderlands Campaign coordinator for the Sierra Club. The slotted barriers have frequently trapped debris during rainstorms, including in Organ Pipe in 2008 and 2011, turning the “so-called porous walls a solid dam”, said Millis. There are also plans to pump water from underground aquifers to make concrete.

The impact could be most grievous at the cherished Quitobaquito Springs. This oasis on the border, one of the oldest inhabited places in North America, is home to the only US populations of the endangered Quitobaquito pupfish and Sonoyta turtle.

“It won’t take much to dry them,” said Dahl, standing amid the willows and cottonwoods that surround the spring-fed pond and provide some of the only shade in an otherwise treeless landscape.

“Pumping water out of the desert at Organ Pipe Cactus national monument, on federally protected land, to support this project is a crime against the American spirit and will do lasting damage to a national treasure,” the Arizona congressman Raúl Grijalva said in an email to the Guardian. “Congress has to step in and stop this.”

Existing border fence at Organ Pipe Cactus national monument near Lukeville, Arizona, on 16 February 2017, on the US-Mexico border. Photograph: Jim Watson/AFP/Getty Images

The government’s ability to build in protected areas along the Mexican border is unique. A 2005 law grants DHS the power to waive any laws “necessary to ensure expeditious construction” of border barriers. It has been used ever since. The Trump administration has waived numerous state and federal laws, including the Endangered Species Act and the Clean Air Act, to construct barriers in protected areas in every southern border state.

Ongoing litigation by environmental and immigration rights groups could halt construction.

Dahl worries it will be too late. Standing near Quitobaquito Springs and looking toward nearby Mexico, he contemplated what is at risk.

“This is one of the true gems of the Sonoran desert,” he said. “It would be a tragedy if it all was lost for an unnecessary and deadly wall.”