Outside Miami‘s Biscayne Bay, coral reefs that were once a vivid rainbow have been turned a barren gray, choked in sediment, by a dredging operation run by the U.S. Army Corps of Engineers.

The Port of Miami is dredging its shipping channel in the hope of luring the mammoth cargo ships that will sail through the widened Panama Canal when that work is finished in 2016. Port Everglades in neighboring Fort Lauderdale, which is even richer in coral than Miami, plans to dredge its channel in two years.

Up and down the East Coast, ports are competing to attract the “post-Panamax” freighters, but South Florida is different: The dredging here inflicts damage—some say irreparable damage—on North America’s only coral reef tract. The reefs offer habitat for diverse marine life, a buffer against rising seas, and a $6 billion economic engine.

The state government and industry leaders back the $210 million dredging operation, which is scheduled to be finished by August. But critics say coral should not be sacrificed in the quest to attract ships that may not come.

The Florida reefs are already under siege from acidification, human activity, and climate change, conservationists say. They’ve sued the Army Corps of Engineers, arguing it failed to safeguard staghorn coral and elkhorn coral, which are protected under the Endangered Species Act.

The damage comes not just from the dredge slicing into reefs, says coral biologist Andrew Baker of the University of Miami. Coral are being killed over a much wider area by sediment stirred up by the dredging and dropped from scows that are carrying it offshore for disposal. Heavy sediment from dredging could linger for years in the bay’s slow-moving waters, hurting sea grass and aquatic life.

“The corals that were killed were decades old,” Baker says. “It’s going to take decades for them to come back.”

Boon or Bust?

The port is deepening the shipping channel from about 44 to 52 feet (13 to 16 meters) as part of a $2 billion overhaul. The renovations will create more than 30,000 jobs and make Miami the first post-Panamax port south of Virginia, supporters say. Fort Lauderdale and Jacksonville, Florida; Savannah, Georgia; and Charleston, South Carolina, plan to expand their shipping channels in the next several years.

“This is a once-in-a-century opportunity,” says Leticia Adams, public policy director for the Florida Chamber of Commerce.

But Chris Byrd, a former state environmental attorney, argues that coral shouldn’t be collateral damage in a speculative gamble. The big ships could bypass Miami anyway, he says, because it’s less profitable to unload freight at the peninsula’s southern tip and haul it overland for hundreds of miles. Jacksonville will finish its deep channel later, but it’s farther north, Byrd says—and it doesn’t have coral reefs to destroy.

The reefs in South Florida run 358 miles (576 kilometers) along the coast, from south of Key West to north of Palm Beach. The Miami reefs are just outside Biscayne Bay. The dredge is slicing through seven acres of reefs as it deepens a shipping channel from the ocean to the port inside the bay. It will widen a quarter-mile stretch by 300 feet (91 meters). Another vessel sucks up sediment from the dredging, then loads it onto scows that carry it to a dumpsite five miles (eight kilometers) offshore.

In advance of dredging, the corps transplanted more than 1,100 coral colonies—including 38 threatened staghorn. Most were moved to other reefs, and about 160 were taken to a nursery at the University of Miami to regrow, Army Corps of Engineers spokesperson Susan Jackson says.

The corps built artificial reefs near the dredged area to replace some of the natural reefs that were lost, Jackson says, plus a 17-acre sea grass bed inside the bay to help make up for meadows killed by dredging.

The corps’s permit allows light sediment to fall within a 150-meter (164-yard) distance of the shipping channel. State regulators issued the corps a warning last year after divers observed heavy silt covering coral over a much wider area. The inspectors also found that traps intended to catch and measure sediment were disabled. And some of the boulders dropped to build artificial reefs had crushed coral and sponges.

The state has yet to order corrective action.

“Meanwhile, they dredge and dredge and dredge,” says Biscayne Bay Waterkeeper Rachel Silverstein, a conservationist and marine biologist who filed the lawsuit.

Watery Moonscape

One day last month Silverstein, videographer Katie Cleary, and I went for a dive about 250 meters (820 feet) north of the shipping channel and two miles (three kilometers) off the Miami skyline. As we prepared to go in the water, a scow loaded with dredged sediment cruised past our boat. The corps and the Environmental Protection Agency have reported excessive leaking and other problems with the scows hauling sediment to the dumpsite.

On the bottom, we saw reef after reef caked in sediment, forming a gray moonscape, devoid of the normal vivid hues. Silt covered diploria (known as brain coral) and meandrina (maze coral) and engulfed leafy gorgonian coral. It filled crevices and nooks that provide habitat for fish, shrimp, rays, eels, snails, and crabs.

Silverstein found staghorn coral with a tag—the corps had transplanted it here, supposedly out of harm’s way, a year ago. It looked sickly.

At another reef, Silverstein grabbed a handful of silt. The gray sand was laced with a dark, sticky residue. That dark sediment, Silverstein said later, is a dredging byproduct that blocks oxygen as well as sunlight, suffocating coral and microorganisms. Sediment coating the reefs stymies red-encrusting coralline algae that feed fish, urchins, and mollusks and are vital to the reefs’ health and recovery.

Countless threatened corals were never rescued, she said, and those that were transplanted are choking in sediment. “There’s no end in sight to the sediment damage,” Silverstein said.

Murky Future

The corps must assess damage in Miami a year after dredging is finished, Jackson says, and if sedimentation lingers that long, it has to take further action. She said the corps is always exploring new ways to ease environmental impacts. For instance, growing nursery corals to replace ones lost in dredging was unheard of a few years ago, she says.

Despite the controversy in Miami, the National Oceanic and Atmospheric Administration (NOAA) backs the corps’s request to dredge Port Everglades, where more coral would be affected.

NOAA approved the plan to enlarge the Port Everglades channel, mainly because it calls for planting more than 100,000 nursery-grown corals to replace those destroyed in dredging and to enhance depleted reefs in that area, says David Bernhart, NOAA’s assistant regional administrator.

The University of Miami’s Andrew Baker hopes the agencies will learn from the Miami project’s failings when they dredge Port Everglades. That would include giving research teams like his more time to rescue corals and requiring scows to drain water from sediment loads farther from shore instead of over the reefs—which inevitably drops fine sediment on the corals.

As it was, Baker and his team rescued 1,200 coral colonies in Miami in addition to the ones transplanted by the corps. The team moved the corals—most of them weakened from bleaching—to a university lab where researchers could care for and analyze them.

Baker’s team is studying whether bleaching, in which corals spontaneously expel the microorganisms that live inside them and provide them with energy, might be an adaptive response to warming water rather than just a symptom of degradation. Baker thinks the Miami corals are a hardy sort that could offer insight into how more fragile corals might be preserved as climate changes—a good argument for studying them, he says, rather than wiping them out.