It’s a few hours before dawn in the Peruvian rainforest, and five bare light bulbs hang from a wire above a 40-foot-deep pit. Gold miners, operating illegally, have worked in this chasm since 11 a.m. yesterday. Standing waist-deep in muddy water, they chew coca leaves to stave off exhaustion and hunger.

In the pit a minivan-size gasoline engine, set on a wooden cargo pallet, powers a pump, which siphons water from a nearby river. A man holding a flexible ribbed-plastic hose aims the water jet at the walls, tearing away chunks of earth and enlarging the pit every minute until it’s now about the size of six football fields laid side by side. The engine also drives an industrial vacuum pump. Another hose suctions the gold-fleck-laced soil torn loose by the water cannon.

At first light, workers hefting huge Stihl chain saws roar into action, cutting down trees that may be 1,200 years old. Red macaws and brilliant-feathered toucans take off, heading deeper into the rainforest. The chain saw crews also set fires, making way for more pits.

This gaping cavity is one of thousands being gouged today in the state of Madre de Dios at the base of the Andes—a region that is among the most biodiverse and, until recently, pristine environments in the world. All told, the Amazon River basin holds perhaps a quarter of the world’s terrestrial species; its trees are the engine of perhaps 15 percent of photosynthesis occurring on landmasses; and countless species, including plants and insects, have yet to be identified.

In Peru alone, while no one knows for certain the total acreage that has been ravaged, at least 64,000 acres—possibly much more—have been razed. The destruction is more absolute than that caused by ranching or logging, which accounts, at least for now, for vastly more rainforest loss. Not only are gold miners burning the forest, they are stripping away the surface of the earth, perhaps 50 feet down. At the same time, miners are contaminating river...