Florida’s coral reefs are facing what could be an unprecedented threat from a marine heat wave that is warming the Gulf of Mexico, pushing water temperatures into the 90s Fahrenheit.

The biggest concern for coral isn’t just the current sea surface temperatures in the Florida Keys, even though they are the hottest on record. The daily average surface temperature off the Keys on Monday was just over 90 degrees Fahrenheit, or 32.4 Celsius, according to the National Oceanic and Atmospheric Administration.

The real worry, scientists say, is that it’s only July. Corals typically experience the most heat stress in August and September.

“We’re entering uncharted territories,” Derek Manzello, an ecologist and the coordinator of NOAA’s Coral Reef Watch program, said.

Coral reefs are natural wonders that support myriad species and blunt damage from storms. In the United States, reefs generate economic benefits to the tune of $3.4 billion annually for fisheries, tourism and coastal protection, according to NOAA.

But oceans have absorbed some 90 percent of the additional heat caused by humans as we burn fossil fuels and destroy forests. When sea temperatures rise too high, corals bleach, expelling the algae they need for sustenance. If waters don’t cool quickly enough, or if bleaching events happen in close succession, the corals die. For decades, scientists have been warning that climate change is an existential threat to coral reefs. Already, the world has lost a huge proportion of its coral reefs, perhaps half since 1950.

“To be blunt, it can be very depressing,” Dr. Manzello said. “Unfortunately, I’m a scientist watching it happen.”

Marine heat isn’t just affecting the Gulf of Mexico. Globally, about 40 percent of the planet is experiencing a marine heat wave, according to Dillon Amaya, a physical scientist at NOAA who studies them.

“Florida is one patch in a terrible quilt right now,” Dr. Amaya said.

In part, that’s because the planet is entering a natural climate phenomenon known as El Niño, which typically brings warmer oceans. But now, El Niño is coming on top of long-term warming caused by greenhouse gas emissions.

While coral is especially vulnerable, heat waves harm untold species, and the effects are different around the world, as species are adapted to different temperature ranges.

In general, fish need more oxygen when the water is warmer. That’s a problem, because warmer water holds less oxygen.

“Large-scale fish kills are becoming more frequent as our climate changes,” Martin Grosell, a professor of ichthyology at the University of Miami, said.

Coral reefs are particularly important because so many species rely on them. About 25 percent of all marine life, including more than 4,000 kinds of fish, depend on reefs at some point in their lives, according to NOAA.

While there aren’t yet reports of bleaching in Florida, it has already begun on reefs to the south, Dr. Manzello said, off Belize, Mexico, El Salvador, Costa Rica and Colombia.

Florida’s coral reef system stretches about 350 miles, from the St. Lucie inlet on the mainland south and west past the end of the Keys, and is frequented by sea turtles, manta rays, flounder and lobster.

What happens in Florida will depend on conditions over the next few weeks. Storms, which churn up deeper, cooler water and reduce sunshine, could provide relief, scientists say. El Niño periods are typically associated with below-average Atlantic hurricane seasons, but that might not hold true this year.

Researchers who care about coral are deeply troubled.

“I do lose sleep over it,” said Andrew Baker, a professor of marine biology at the University of Miami, where he directs the Coral Reef Futures Lab. “But I don’t want to write the eulogy just yet.”

Scientists like Dr. Baker are racing to come up with ways to help coral become more resilient to higher temperatures, for example by crossing Florida’s corals with varieties that seem to withstand more heat. But ultimately, the survival of corals and countless other species relies on the ability of humans to rein in climate change.

“You have to go to the root causes,” Lizzie McLeod, the global oceans director at The Nature Conservancy, said. “We have to be reducing emissions, we have to move to clean energy, we have to reduce subsidies to the fossil fuel industry.”

In Key West, beachgoers expressed surprise at the warmth of the ocean, comparing it to bath water. Lynsi Wavra, a captain and ecotour guide, said her mother had lived there for 20 years and had witnessed the coral declining.

“She’d come home crying,” Ms. Wavra said.

Frances Robles contributed reporting.