I flew over the Peruvian Amazon two years ago, in a small propeller plane. An aerial perspective gives you a true sense of the rainforest’s scale, as treetops stretch from one horizon to another like an infinite and unbroken array of broccoli florets.

But from the air, the damage to the jungle also becomes more obvious. We flew over charred hectares of burnt trees, huge piles of felled logs and, most memorably of all, vast (and mostly illegal) gold mines.

Before the flight, I might have pictured a gold mine as a surreptitious doorway carved into a mountainside. The largest of the ones I saw, known as Guacamayo, was more like a pustulent wound—a gash of festering yellows and whites amid the lush greens of the jungle. It even seeped into the nearby river and jaundiced its water. It was a nauseating sight, and one utterly disconnected from the glistening metal that gets fashioned into jewellery and ornaments.

The Madre de Dios region of southern Peru is rich with both life and gold, and the latter threatens the former. A recent gold rush, prompted by skyrocketing prices and enabled by a new highway, have brought tens of thousands of hopeful miners to the region. Back in 2009, scientists showed that the three big mines—Huepetuhe, Guacamayo and Delta-1—had already claimed 15,500 hectares of forest, and were growing at a rate of 1,900 more every year.

But Greg Asner from the Carnegie Institution for Science—the same scientist who flew me over the Amazon—has found that the situation is even worse. The big mines like Guacamayo are an obvious problem, but thousands of smaller ones have sprung up in the last few years. They’re extremely hard to find or control, and Asner found that they collectively account for more than half the gold-mining in the region.

“The Ministry of Evnironment estimates that there are 50,000 to 70,000 of these miners in the region,” says Asner. “They’re working on groups of three to ten, so that’s a lot of mining.” Everyone was focusing on the big, gaping wounds, and ignoring the subtler infections creeping through the Amazon’s skin.

The small mines look like deep pits in forest clearings, up to 10 metres deep with debris and mud at the bottom. The miners cut down a small stand of trees, dig away the top layers of soil and blast away at what remains with high-pressured water. They transfer the resulting slurry into an oil drum and add mercury. “Someone stands in the drum and starts jumping up and down. It’s like squishing grapes,” says Asner.

The mercury binds to any gold in the mud, which the miners filter out with a pan. The nuggets are dried and heated, releasing even more mercury into the air as a vapour. It’s no surprise that the miners often suffer from mercury poisoning, as do people who live in nearby towns or settlements, or downstream of polluted rivers. And yet, they get gold. “Five days ago, I ran into an old Peruvian student on the river, and he told me that in some places, there’s half a kilo of gold per hectare, deep down below the forest floor,” he says.

The miners are getting craftier. They’re setting their mines back further and further from the edges of roads and rivers, and clearing away only small patches of trees. “As you go up and down the river, you don’t see anything,” says Asner, “and the methods that are used to map mines from satellite imagery are insensitive to small clearings.”

So, Asner turned to CLASlite—a piece of software he built to detect the signs of logging on satellite images. He trained the system to identify the signatures of small gold mines, and applied it to images that had been collected since 1999.

View Images This CLASlite map shows the areas along the Madre De Dios river damaged by small, clandestine gold miners between 1999 and 2012. Credit: CLASlite Team

The images showed that gold mines in Madre de Dios have quintupled in coverage since 1999, from 10,000 hectares to more than 50,000 now. The three big mines are a problem, but the smaller ones have multiplied so quickly that they now account for 51 percent of mining in the area.

The mines are also expanding faster than anyone had thought—from a rate of 2,166 hectares per year before the gold price boom of 2008, to a current rate of 6,145 hectares per year. Those estimates are around 40 percent higher than any previous ones for the region, and they mean that gold mining is now the biggest cause of deforestation in the region, beating out logging or farming. (And that’s ignoring the fact that mining increases the odds of ranching, farming, bushmeat hunting, and environmental damage in nearby areas.)

Worse still, the mines are encroaching into new habitats. The big mines like Guacamayo are most found in swampy regions near the main rivers, but the smaller operations are heading deeper into the forest, and higher up the foothills of the Andes. These regions host very different communities of plants and animals, which are now being threatened. The mines are also spreading further up-river, which threatens to pollute more of the waterways with mercury.

To verify the satellite results, Asner’s team started checking out some of the supposed mines on the ground. “It’s extremely stressful going into these places,” he says. When he visited Guacamayo, he did so at a quiet time of day, and wearing a hoodie. The smaller mines are even more treacherous. “There are reports of people shooting or machete-ing each other, which I cannot confirm. But it’s definitely not comfortable, and the miners are very quick to threaten.”

Since the field surveys were so dangerous and time-consuming, the team also took to the skies. That is, after all, where Asner does most of his research. His small plane—the Carnegie Airborne Observatory—is fitted with a trio of sensors that can map the shape of a forest’s trees down to their individual branches, measure the chemical composition of their leaves and trunks and soil, and even identify species from these chemical signatures. (I profiled him, and wrote about his work, for Wired UK last year.)

The surveys confirmed that the satellite images are capturing between 84 and 94 percent of the mines in the area, and just 7 to 18 percent of the ones they identified are false positives. For the most part, the technique is accurate and reliable.

“Asner’s study helps further raise awareness about continued illegal gold mining in this area,” says Jennifer Swenson from Duke University, who ran an earlier mapping study of the three big mines. “[We now need] to focus on how to develop policies or strategies to at least decrease the mining rate, as well as miner education and policies to reduce the use of mercury and subsequent contamination.”

“It gives us a clear idea about the scale of the challenge,” says Ernesto Ráez Luna, a scientist from Peru’s Ministry of the Environment (MINAM) and a co-author on the new study. “We knew that illegal mining was taking place, but not how fast it was moving into the forest. We now know the velocity.”

Doing something about it is another problem, but Luna says that MINAM is pursuing several avenues. For a start, they want to prosecute the bosses who control the large proportion of the illegal mining operations, and push for harder jail sentences. “What used to be small-scale mining has been infiltrated by crime,” he says. “We don’t want to go after the labourers, who include a large number of sincerely poor people. We want to focus on the few at the top of the pyramid.”

They also want to formalise the small-scale mines, and help people who want to work lawfully to create proposals for environmental management. And they want to help those who are trapped in their current situations. “We also need to do social restoration, as well as ecological restoration,” says Luna. “The illegal mining has brought with it a number of other crimes, including slave-labour and sexual exploitation of minors.”

Asner adds that three other moves might help. First, rein in mining permits; these are current the responsibility of regional governments and they are given out freely, perhaps even aggressively. Second, limit the amount of fuel that’s delivered to the Puerto Maldonado, the region’s capital. Currently, Madre de Dios actually consumes more fuel than the Lima, Peru’s capital city, because gold-mining is so big. Finally, stem the import of mercury, much of which comes in via the black market.

Reference: Asner, Llactayo, Tupayachi & Luna. 2013. Elevated rates of gold mining in the Amazon revealed through high-resolution monitoring. http://dx.doi.org/10.1073/pnas.1318271110

If you want to read more about gold-mining in Peru, do read these two excellent pieces: