The discovery, announced Friday in the journal Science, was more than three decades in the making. Patricia Yager, a professor of oceanography and climate change at the University of Georgia, and the sole American researcher on the project, wasn’t even in the area to look for reefs, at first. Her project was supposed to use the RV Atlantis to investigate how the Amazonian plume affects the ocean’s absorption of carbon dioxide. (The Atlantis is the “host vessel” of the deep-water submarine Alvin, the same craft that discovered the wreck of the Titanic.) But one of the senior Brazilian scientists, Rodrigo Moura, said that he wanted to use their time on the vessel to look for a reef he thought might be in the region.

(Yager’s expedition was repeatedly denied access to the mouth of the Amazon by the Brazilian government, so she had added Brazilian oceanographers to the cruise in hopes of securing its approval.)

“I kind of chuckled when Rodrigo first approached me about looking for reefs. I mean, it’s kind of dark, it’s muddy—it’s the Amazon River,” Yager told me. “But he pulls out this paper from 1977, saying these researchers had managed to catch a few fish that would indicate reefs are there. He said, ‘Let’s see if we can find these.’”

Moura would need a dredge to look for a reef, but Yager hadn’t even planned on taking one on the journey. She wasn’t sure she had access to one. But after Moura convinced her, she remembered that there was a “big old dredge” sitting on the back deck of the oceanography building at the University of Washington, her alma mater. They shipped it across the country in time for the cruise.

Timing would be tight no matter what. The Atlantis had to get from Barbados to the Amazon and back in two and a half weeks, and most of that time would be spent on its original goal. But Moura paid attention to the seabed sonar throughout the cruise, Yager said, and when they wound up with some extra time, he knew where he wanted to put down the dredge.

It came up with corals, sponges, stars, and fish—there had been a coral reef below them all along. “I was flabbergasted, as were the rest of the 30 oceanographers,” said Yager. There appeared to be a thriving reef at the mouth of the Amazon, beneath some of the muddiest water in the world.

Part of what surprised the researchers is that the reef could exist at all, because all the gunk in the Amazonian plume often sheltered it from the sun. Later cruises by Moura and other Brazilian researchers have indicated that the reef’s biology varies depending on its location. The southern section is only covered by the plume three months of the year, so its environs can complete more photosynthesis. (Most corals live in symbiotic relationships with photosynthetic algae that inhabit their pores.) The southern section contains more staghorns and other colorful corals, “much more what you might imagine a coral reef would look like,” says Yager. The north section, dominated by sponges and carnivorous creatures, is shielded from sunlight by the muddy plume more than half of the year.