Biscayne Bay Is Slowly Becoming the Ocean

In the shadow of Miami’s skyline, in water churned daily by boats and jet skis, juvenile great hammerhead sharks—a critically endangered species—spend the first two years of their lives. A few miles from downtown, researchers recently pulled a 12-foot critically endangered sawfish from the same shallows. The species has been dying off in alarming numbers across South Florida’s waters since 2024, in an event scientists suspect was set in motion by record ocean heat. 

The bay teems with life most of the city never registers: more than 30 endangered or imperiled species and over 100 that matter to commercial and recreational fishing. Yet when researchers surveyed more than 1,000 Miami-Dade residents, most rated the bay as “moderately healthy,” even as its water quality had measurably declined and a government assessment warned the estuary had reached “a tipping point.”

It is also changing in ways almost no one can see.

Over the past two decades, the bay has grown warmer, saltier and more acidic, according to a new University of Miami study that analyzed 20 years of monthly water quality readings. The shifts are real but gradual—too slow for even the divers, anglers and scientists who spend their lives on the water to see directly. “Since I have been here, the bay has been salty,” said Ana Zangroniz, a Florida Sea Grant agent who has worked on the bay since 2017, describing change so incremental it goes unnoticed. 

What the eye misses, the data captures: a bay sliding steadily from an estuary to something closer to the open ocean, a transition the study’s authors say sea-level rise has made effectively irreversible. 

The bay’s fish are already registering the shift. Joseph Serafy, a NOAA research fishery biologist who has tracked Biscayne Bay fish communities for two decades, has watched the catch change as the water grows saltier. Snook, seatrout and mullet—species that thrive where fresh and salt water mix—have declined, he said, while fish that tolerate a wide range of salinity, like gray snapper and grunts, hold on. It is the signature of a bay tilting away from its estuarine past: As the brackish conditions vanish, so do the creatures built for them.

Meanwhile, median water temperatures rose half a degree Celsius bay-wide over the two decades the scientists analyzed, and nearly twice that (0.8 degrees Celsius) in the North Bay, the most urbanized and poorly flushed stretch of water. 

But the slow climb in averages is not what worries Serafy most. It masks a more dangerous trend of sharper, more frequent extremes. Cold snaps, heat waves, stretches of hypersalinity and sudden crashes in oxygen do the real damage, and a warmer, saltier baseline makes each spike more punishing, according to Serafy.

The summer of 2023 showed what that looks like. A marine heat wave drove water temperatures off South Florida to levels never before recorded, including a reading of 101 degrees Fahrenheit in shallow Manatee Bay that may have been the hottest seawater ever measured. The region’s coral reef was bleached from end to end. Warm water holds less oxygen; so does salty water. When both climb at once and seagrass dies back, fish can suffocate, the mechanism behind die-offs that Manatee Bay had seen before.

The pattern traces back, in part, to how South Florida moved its water. A century of canals replaced the sheet flow—the slow, shallow film of freshwater that once spread across the Everglades miles wide instead of rushing through canals—that once seeped into the Biscayne Bay along a broad brackish shoreline with abrupt, pulsed releases that swing salinity up and down. Restoring that gentler, more consistent flow is among the central goals of the multi-billion-dollar Everglades restoration effort.

For the hammerhead sharks, the danger runs through their food. Juvenile great hammerheads depend almost entirely on the bay for their first two years, feeding on a narrow diet of small stingrays and other bottom dwellers, animals that themselves eat the crabs, mollusks and shelled creatures that are most vulnerable to acidifying water. 

“Acidification has the potential to affect both sharks themselves physiologically and prey species that are important to them,” said Catherine Macdonald, director of the Shark Research and Conservation Program at the University of Miami, whose team documented the nursery. When the base of a food pyramid shrinks, she explained, everything above it must shrink too: “The shark population has to shrink in response, definitionally, because the energy is not in the system to support them.”

Macdonald’s larger fear is starker. The bay’s hammerheads return to the same waters to give birth; if those waters become unsuitable, an entire genetic lineage could vanish with them. “I really deeply hope that we don’t end up [with] the first nursery that is reported to disappear because of climate change,” she said.

What is happening in Biscayne Bay is not unique, but it’s not universal either. A landmark 2020 study tracked 166 estuaries along Australia’s coast and found them changing faster than global climate models predicted, too small and shallow for the models’ coarse grids to capture. 

“These coastal habitats are often quite shallow,” said lead author Elliot Scanes of the University of Technology Sydney. He explained that shallow waters heat faster than larger, deeper environments; “they’re like a puddle in the sun.” 

But direction depends on geography: Australia’s small estuaries have been freshening as rainfall rises, while Biscayne Bay, large and increasingly fed by the sea, is going the other way. 

“As sea level rises, there will be more saltwater intrusion,” Scanes said, “and it’s foreseeable that maybe they’ll turn into just a big oceanic bay.”

That intrusion is the change the study’s lead author fears most, and it is the one that reaches beyond the water’s edge. For oceanographer Josefina Olascoaga, the concern that keeps surfacing is fresh drinking water. The same salt creeping into the bay is pressing into the Biscayne Aquifer, the porous limestone that supplies freshwater to most of South Florida.

It is the most consequential shift of all, and the hardest to see. Some coastal wells have already been abandoned to the intruding salt; cities from Hallandale Beach to Hialeah have drilled inland to stay ahead of it. 

The bay has spent 20 years showing the change at its surface. Underground, the same salt is moving toward the water Miami drinks.