© 2025 All Rights reserved WUSF
Play Live Radio
Next Up:
0:00
0:00
0:00 0:00
Available On Air Stations
Our daily newsletter, delivered first thing weekdays, keeps you connected to your community with news, culture, national NPR headlines, and more.
Climate change is impacting so much around us: heat, flooding, health, wildlife, housing, and more. WUSF, in collaboration with the Florida Climate Reporting Network, is bringing you stories on how climate change is affecting you.

Wasting Away: The die-off

A dead manatee laying on a brown tile floor
Florida Fish and Wildlife Conservation Commission
A dead mother manatee, found in the Indian River Lagoon by two state scientists, awaits examination in a lab in early 2021 during the beginning of the starvation die-off.

Rampant pollution caused manatees to starve. Florida waters are getting worse.

Perched on a spit of land, two biologists peered into slate blue water. Below them, manatees floated like clouds, raising whiskery snouts to let out long, loud breaths.

The Indian River Lagoon looked like an ideal symbol of Florida. But by that afternoon in late January 2021, the scientists knew they stood at the edge of catastrophe.

For decades, the beloved animals had survived winter by retreating to this pocket of the Lagoon near Cocoa, where discharges from a power plant kept them warm. They grazed on seagrass that swayed in gentle currents.

Quietly, though, their sanctuary changed. The seagrass disappeared. Barrens of sand stretched for miles, like an underwater desert.

Dozens of dead manatees washed up in Brevard County, and state scientists scrambled to figure out why. The biologists scanned the rippling water. It didn't take much time to find another carcass.

This one was a mother, about 9 feet long, rolled on her back. Her body looked thin. Her belly curved inward. Her head was sunken and misshapen like a peanut.

When researchers cut into her remains, they discovered much of her fat had wasted away. Her gut was watery, as if she’d dissolved from within. She should have weighed at least 1,000 pounds but was just 650.

She’d starved.

A pair of manatees, a mother and calf, swim underwater
Douglas R. Clifford
/
Tampa Bay Times
A mother manatee and calf swim near Three Sisters Springs in Crystal River on Florida’s Gulf Coast.

Over the next two years, hundreds of manatees would experience the same brutal,  yet avoidable, fate. Their main food source vanished after decades of pollution flooded the Lagoon — and the species’ most important home on the East Coast turned into a graveyard.

For nearly a half-century, lawmakers and environmental regulators in Tallahassee have known that rampant nitrogen and phosphorus contamination wreak havoc on precious Florida waters.

But they’ve failed to control runoff from major industries, allowing the Lagoon and hundreds of waterways to become dangerously polluted, a Tampa Bay Times investigation has found.

To trace the manatee die-off to its roots, Times reporters conducted a first-of-its-kind statewide analysis, pinpointing alarming levels of chemicals in nearly 1 in 4 waterways.

The Florida Department of Environmental Protection touts spending millions of dollars to reduce the contamination.

But the efforts aren’t working, the Times found.

More than half of tainted waterways analyzed by reporters either showed worsening levels of pollution or weren’t getting better over the last two decades.

Florida regulators haven’t created targets for curbing contamination in most of them. And even where officials have stepped up efforts, more of the waterways have been getting dirtier instead of cleaner.

The trends should prompt state leaders to take swift action, said Elizabeth Southerland, a retired U.S. Environmental Protection Agency official who finished her 33-year career leading the office in charge of water quality standards.

“They should be alarmed,” she said.

The Department of Environmental Protection declined to make its secretary or staff available for interviews. Alexandra Kuchta, a spokesperson for the agency, provided multiple statements and answers to questions in writing.

The statements acknowledged that increasing pollution across the state is a matter of concern. But the department said environmental change takes time, both for waterways to reach disastrous tipping points and to show improvement. The agency applauded restoration efforts and environmental laws supported by Gov. Ron DeSantis, saying the moves have set up regulators for success.

“For decades, stakeholders have languished over the need for greater funding and policies dedicated to protecting Florida's environment,” the department said. “Now we have it, strongly positioning DEP and its partners with the tools needed to move Florida forward.”

But the cleanup measures are far from comprehensive. Florida’s biggest sources of water pollution — agriculture and development — aren’t held to strict limits on the nitrogen and phosphorus that flow off sprawling farms and city streets. Chemicals spew from fertilizer and waste, eventually reaching fragile waters.

The Times found that every year, an estimated 100 million pounds of nitrogen and 4.5 million pounds of phosphorus could mar already contaminated waters, from the Panhandle to Miami.

That includes more than 3 million pounds of nitrogen and 400,000 pounds of phosphorus around the Lagoon — much of it from runoff. Developers and farmers have transformed tens of thousands of acres into subdivisions, ranches and shopping plazas over the last four decades.

Such contamination isn’t the type that draws quick condemnation like an oil or wastewater spill. It imposes a more insidious toll, one that can go unnoticed until it eventually explodes.

At appropriate levels, nitrogen and phosphorus are building blocks of a healthy environment — fuel for plants and animals alike. But in excess, they feed eruptions of algae that poison fish and kill seagrass, destroying habitats for manatees, turtles and dolphins.

More than 89,000 acres of seagrass disappeared statewide over roughly a decade, the Times found, including from waters beset by recent blooms such as Tampa Bay and Charlotte Harbor. In the Lagoon, nearly all the seagrass manatees could have eaten died. The extent of seagrass lost across the state during that time has not been tallied by a news organization until now.

Lush seagrass is shown underwater
Douglas R. Clifford
/
Tampa Bay Times
Lush seagrass is shown in a section of the Indian River Lagoon that has seen the plant make a comeback. Algae blooms, fueled by pollution, caused tens of thousands of acres of seagrass in the Lagoon to disappear.

It's hard to overstate the importance of seagrass to Florida. Beds help protect shorelines against erosion from tropical storms. Even just a few acres can make water clearer and nurture countless species, from tiny crabs to hulking tarpon.

Remove the seagrass, and the ecosystem topples.

Curbing pollution is supposed to reduce the risk of algae upending the environment — akin to people lowering their cholesterol to decrease their chance of developing heart disease.

Under the federal Clean Water Act, states hold responsibility for limiting much of the runoff that fouls waters. But despite receiving billions in federal funding, governments across the country have struggled to make improvements from the Chesapeake Bay to the Great Lakes to San Francisco Bay.

Man in an orange vest standing over dead manatees piled up inside a large trash bin
Florida Fish and Wildlife Conservation Commission
Dead manatees pile up inside a large trash bin near the Indian River Lagoon. Researchers performed examinations on the ground as they hurried to handle an overwhelming number of carcasses.
A group of black birds flying in the sky
Florida Fish and Wildlife Conservation Commission
Vultures circle a trash bin filled with dead manatees. Some carcasses were brought to the county landfill during the die-off’s peak. Others were left to decay in remote parts of the Lagoon.

“If it happened in the Indian River Lagoon, it could happen anywhere,” said Duane De Freese, executive director of the Indian River Lagoon National Estuary Program, a government conservation group.

When emaciated manatees started to turn up dead, scientists in Florida’s wildlife agency quickly suspected poor water quality as the culprit. They called the Lagoon “an estuary in crisis.”

For two winters, they threw lettuce into the water to stave off more death. Researchers will never know exactly how many animals starved during the die-off’s peak — only that it hollowed out generations of a threatened species last estimated to have a population below 12,000.

During some months, so many carcasses washed up that researchers could barely keep pace. They hastily examined dozens of manatees on the ground and stacked remains in a long, rusty trash bin as vultures circled overhead. Others were left to decay in quiet stretches of the Lagoon. One sandy bend of Merritt Island became littered with bones.

Famished manatees showed telltale signs: ribs visible through sagging skin, deformed heads, round bellies gone flat.

The day biologists found the dead mother in January 2021, they saw the increasingly familiar — and harrowing — markers in her. But they also discovered something else: a view into how long the disaster could endure.

Staring into the water, the scientists noticed the mother was not alone. A baby swam around her, nuzzling close.

They realized they’d come across an orphan, hungry and confused, trying to get milk from the carcass.

There wasn’t much daylight left. They had to act fast or the calf could die, too. The first step to saving her was obvious.

Get her out of the Lagoon.

A drone image shows homes along a lagoon
Luis Santana
/
Tampa Bay Times
A drone image shows homes along the Indian River Lagoon in Titusville. Tens of thousands of acres of land around polluted sections of the waterway have been transformed by development and agriculture.

Pollution's long tail

The vast majority of manatees on the East Coast depend on the Lagoon, sheltering in its shallows and gliding down it like a marine highway.

At a glance, the waterway resembles a picture ripped from a travel magazine. It stretches from around Jupiter to New Smyrna Beach, a 156-mile jewel shaped like a hairpin.

In the south, mangrove islands near the mouth of the St. Lucie River are home to pelicans, herons and frigatebirds, whose throats inflate like crimson balloons. Silent Mosquito Lagoon to the north flashes with redfish and mullet.

Below the surface, swaths of the Lagoon floor are smothered by several feet of dark ooze. Scientists call this emblem of pollution’s long tail “muck” or “black mayonnaise.” It regularly releases stored nitrogen and phosphorus — old contamination mixing with new.

A close-up of a hand with muck on fingers
Douglas R. Clifford
/
Tampa Bay Times
Indian Riverkeeper Jim Moir displays a handful of muck that he collected on Saturday, Oct. 7, 2023, from the bottom of the St. Lucie River in Martin County.

Like most Florida waterways, the Lagoon’s problems begin on land, where a booming economy over the last century has created an onslaught of pollution.

Change accelerated in the early 1900s when state lawmakers supported building canals and ditches to drain the boggy peninsula. The work allowed for the construction of cattle ranches, citrus groves and homes, according to a report from the Indian River Lagoon National Estuary Program. The canals also linked areas far west to the shore.

Steady growth has churned ever since. Collectively, the transformation more than doubled the amount of land draining to — and polluting — the Lagoon, according to the Estuary Program report.

Animated gif shows acres of transformed land
Aya Diab
/
Tampa Bay Times

More than 30,000 acres around the Lagoon’s now struggling waters were overhauled into lucrative properties such as housing developments, farms and golf courses over the last four decades, a Times analysis of land use and property data shows.

The reshaping of the region mirrors that of the entire state. An estimated 1.9 million acres of natural land were converted into farms, roads, strip malls and subdivisions over the same period. That’s the equivalent of overhauling an area larger than Hillsborough, Pinellas, Pasco and Hernando counties combined.

No animals have been spared the impact — certainly not manatees.

Named the official state marine mammal in 1975, the docile giants have no natural predators. But development has long threatened them, and they were among the first species to be considered endangered.

A number of boats gathered in a lagoon
Douglas R. Clifford
/
Tampa BayTimes
Boaters gather in the Indian River Lagoon, which is not only home to wildlife but also scores of people who live in subdivisions along its shores.

As Florida’s population has grown, so has boat traffic, putting manatees at constant risk. Few survive to adulthood without accumulating a thatchwork of scars from propellers and hulls. Dams block streams that manatees once traversed to reach warm springs. Power plants spit heated water that draws them to unnatural refuges each winter.

Pollution spoils waters they cannot escape.

Development causes compounding problems, destroying wetlands that filter and trap contamination — like nature’s kidneys — at the same time it increases pollution flowing into an overloaded environment.

The Lagoon is especially vulnerable. It moves slowly, pushed by winds rather than major tides. There are few ocean inlets to bring clean, flushing saltwater. Local and state leaders have made conditions even more sluggish by building causeways that block the limited flow.

Once chemicals reach the waterway, they linger. And rain — up to 5 feet a year — is a torrent that acts like a runway for pollution.

A close-up of a putting green in a backyard on water with a boat docked in the background
Douglas R. Clifford
/
Tampa Bay Times
Houses dot canals around the Indian River Lagoon, including one home that has a putting green in the yard. Over the last four decades, tens of thousands of acres around polluted areas of the Lagoon have been transformed into housing developments, farms and shopping centers.

The runoff from downpours mixes with contaminants on the ground: fertilizer spread over fields and front yards, dirty leaves, grass clippings, animal waste, clumps of trash along the road. Where woody hammocks and wetlands once absorbed rainfall, concrete and dirt compacted by development now shed it.

Pipes and ditches are built to spare cities like Titusville and Palm Bay from flash floods during heavy rains. But they also deposit runoff tainted with nitrogen and phosphorus into creeks, canals and the Lagoon with little, if any, treatment.

Even rain that trickles underground picks up chemicals from fertilizer and septic tanks loaded with human waste. More than 100,000 septic systems are buried around polluted parts of the Lagoon, according to state estimates. The dirty water flows through porous limestone and sand, eventually bubbling up at springs or dumping into waterways like the Lagoon.

Together, this type of indirect pollution accounts for most contamination in Florida waters, according to the Department of Environmental Protection.

But America’s signature water pollution law, the Clean Water Act, didn’t address it at the national level. The legislation focused on creating a federal permit system to curb easy-to-trace contamination like discharges from factories and sewage pipes. Ultimately, states were left to handle ubiquitous runoff from cities and farms.

In Florida, regulators have implemented a system using models to estimate the pollution load. But the contamination is rarely measured at its source.

Unlike sewer or factory operators that release wastewater through pipes, the state doesn’t hold most farmers and developers to strict limits on the nitrogen- and phosphorus-laced water that rolls off and sinks below their properties.

Regulators instead push business owners to use methods they believe will reduce pollution, sometimes dangling millions in public funding to share the cost.

Such “best management practices” include limiting fertilizer use when it’s rainy and designing ponds to collect dirty runoff in neighborhoods — even long after developers sell their land.

The Department of Environmental Protection says these methods work. A Times analysis of agency data suggests farmers and ranchers reduce 3.7 million pounds of nitrogen and 336,000 pounds of phosphorus each year by using them.

Another 1.4 million pounds of nitrogen and 403,000 pounds of phosphorus are eliminated by stormwater defenses around cities, such as treatment ponds and local ordinances that restrict use of lawn fertilizer, the analysis shows.

But like the contamination itself, much of these gains are estimates, not measurements — and the water provides a different picture.

A group of pelicans flying over trees with water to the left and a boat in the background
Douglas R. Clifford
/
Tampa Bay Times
Pelicans soar over the Indian River Lagoon, an example of the varied wildlife that call the estuary home.

Ruining Florida's lifeblood

In northern stretches of the Indian River Lagoon, where manatees spend their winters, the water grew increasingly polluted over two decades before becoming a graveyard.

For 10 years straight, phosphorus surpassed the level state records indicate is safe for the environment. Nitrogen concentrations similarly exceeded the state’s healthy threshold.

An imbalance of either chemical puts waterways at higher risk of devastating algae blooms.

Thirty-eight sections in the Lagoon basin are considered polluted by the Department of Environmental Protection, meaning they don’t meet water quality standards set by the state. They’re among more than 1,500 segments across Florida — roughly a quarter of all the state’s waters — tainted by forms of nitrogen, phosphorus or other issues that point to overloads of the chemicals.

See how Florida breaks up water bodies
Regulators divide larger water bodies into smaller segments for analysis.

Charts show how larger water bodies are divided into smaller segments for analysis
Langston Taylor
/
Tampa Bay Times

Reporters analyzed millions of water sampling results that spanned more than two decades. Nearly 800 dirty segments had enough data to identify trends. Fifteen water quality experts vetted the statistical analysis and provided guidance on the Times’ approach.

Across Florida, reporters found that more than half of the waterways showed rising levels of contamination or were failing to get better over the past quarter century.

Steep increases occurred in places that Floridians love and animals depend on to survive.

In tributaries to Old Tampa Bay, a northern stretch of the estuary where anglers find snook and trout, phosphorus concentrations have been on the rise.

In the lower Myakka River, around an island home to threatened wood storks, nitrogen averages have exceeded state standards nearly every year since 2010.

In a Crystal River spring, not far from a spot where manatees huddle by the hundreds each winter, nitrate-nitrite levels have been increasing.

More than half of polluted waterways haven’t shown progress
A third of places the Times analyzed saw improving pollution levels on all problematic chemicals.

Dots show centroids of water body identifiers. In water bodies with trends in multiple chemicals, the highest likelihood for the final category is applied. Read how the Times identified and categorized trends in pollution here.
Shreya Vuttaluru
/
Tampa Bay Times
Dots show centroids of water body identifiers. In water bodies with trends in multiple chemicals, the highest likelihood for the final category is applied. Read how the Times identified and categorized trends in pollution here.

Nitrate is a nitrogen compound found in fertilizer as well as animal and human waste. Nearly three-quarters of springs reviewed by the Times exhibited rising nitrate-nitrite pollution over the last 25 years — including some world-renowned destinations.

“It's getting worse almost everywhere,” said Robert Knight, board president of the Howard T. Odum Florida Springs Institute, a nonprofit advocacy group. “These springs are dying.”

A third of waterways the Times analyzed showed decreasing trends of all chemicals the state says are problematic. Those included places where pollution levels were still too high in at least one of the last three years with complete data, such as the Alafia River near Tampa Bay.

Reporters found another 296 water segments that aren’t identified by the state as contaminated but have been getting dirtier. Several, including a stretch of the Escambia River, recorded nitrogen or phosphorus measurements above state standards.

Environmental regulators don’t typically set targets to reduce runoff pollution in a waterway until chemicals exceed impairment levels. The state’s environmental agency said it follows federal law, which outlines “reactionary” methods to restore waters that are already polluted.

The department develops goals and plans for reducing the chemical load to return to healthy concentrations — a drafting process that can take years. But Florida hasn’t created cleanup targets for more than 1,000 waterways identified as impaired, the Times found.

Even waters with established goals are faltering. Forty-five percent of places reporters analyzed had pollution levels that were increasing or not improving over a decade or more.

Michael Sole, a former secretary for the Department of Environmental Protection, called the lack of consistent gains “embarrassing.”

“Clearly, much more needs to be done,” he said after reviewing the Times’ findings.

A black cormorant under water standing on a thick mat of algae
Douglas R. Clifford
/
Tampa Bay Times
A cormorant swims over a thick mat of algae that covers a bed of seagrass near Fort De Soto in Pinellas County.

In its statements, the department said restoration efforts often don’t deliver measurable progress quickly.

The Times shared its analysis with 33 experts in water policy, hydrology, environmental advocacy and marine biology, including several former state and federal regulators. They said restoring the environment can take decades — and is more difficult in places with deposits of pollution that have settled over many years, such as the Lagoon and Lake Okeechobee. But if the state’s work is effective, contamination levels should begin to drop, and progress can reveal itself within a few years.

“Success is: Did the water quality get better?” said Dave Tomasko, executive director of the Sarasota Bay Estuary Program, a government conservation organization. “If the water quality didn't get better, then you better be able to explain why it's taking so long.”

A drone photograph shows a master-planned community and a sod farm in the background
Luis Santana
/
Tampa Bay Times
A drone photograph shows a master-planned community and a sod farm in the background near the Indian River Lagoon. Agriculture and development are major sources of pollution in the waterway.

When asked for examples of waterways that have met the state’s nitrogen and phosphorus goals, the Department of Environmental Protection referenced 14 lakes in Central Florida as well as a stream and two springs. The agency separately pointed to 118 waters it said are showing progress.

Key stretches of the Lagoon are among those that haven’t reached healthy targets.

Regulators set goals to reduce pollution in the northern and central Indian River Lagoon and the Banana River Lagoon in 2009 — more than 10 years before manatees starved. In 2013, they issued plans for meeting those targets.

Median nitrogen concentrations in the water beyond 0.98 milligrams per liter and phosphorus beyond 0.05 milligrams per liter annually are too high, state records indicate.

Chemical concentrations have increased at the steepest rates in the northern and central Lagoon, the Times found. Those areas are surrounded by more than 180,000 acres of developed land, including the city of Titusville and Viera East, a master-planned community with a golf course and hundreds of homes.

Women in a white hard hat, classes and an orange vest holding handfuls of muck
Douglas R. Clifford
/
Tampa Bay Times
Abbey Gering, associate environmental specialist with Brevard County, holds handfuls of muck, an insidious form of pollution that puts the Indian River Lagoon in danger.
An excavator lifting much out of the water
Douglas R. Clifford
/
Tampa Bay Times
An excavator lifts muck as part of an expensive effort to clean the Lagoon.

The worrying trends aren’t limited to the Lagoon. Across Florida, other contaminated places have been getting dirtier since the state intervened.

They include the Suwannee River, fed in part by springs and surrounded by more than a dozen major farms, and Lake Okeechobee, the state’s largest freshwater lake, where algae blooms threaten animals and slick the surface with green slime.

Like the Lagoon, many worsening waterways are surrounded by thousands of acres of agricultural lands and housing developments, including Rainbow Springs near Ocala and parts of the Little Wekiva River north of Orlando.

The Times found bodies of water getting dirtier even in areas where the state reports progress in curbing runoff.

In the Lagoon, the Department of Environmental Protection estimates polluters reduce more than 500,000 pounds of nitrogen and 100,000 pounds of phosphorus annually, despite flagging water quality in multiple stretches.

In the Caloosahatchee River and estuary, environmental regulators report reductions of nearly 850,000 pounds of nitrogen a year. Yet chemical concentrations have been rising in part of the river near Cape Coral and Fort Myers.

At Jackson Blue Spring in the Panhandle, the state reports cuts of more than 130,000 pounds of nitrogen. But pollution levels regularly averaged more than 10 times the healthy limit.

“It’s what’s on the ground that matters — not what you say, but what you measure,” said Victoria Tschinkel, a former leader of Florida’s environmental agency in the 1980s. “Nature knows what’s going on.”

 Seagrass hangs in a clump on a log in the water
Douglas R. Clifford
/
Tampa Bay Times
Seagrass hangs in a clump in the Indian River Lagoon. Devastating algae blooms killed tens of thousands of acres of seagrass, transforming parts of the waterway into an underwater desert.

The Lagoon snaps

or decades, mounting pollution has disrupted the Lagoon’s natural balance, leaving a vital habitat for manatees susceptible to ruin.

Some of the most contaminated areas suffered crippling algae blooms and seagrass losses.

The pattern has repeated across Florida, according to a Times analysis of regional monitoring surveys and research. Algae block sunlight from reaching seagrass, which depends on photosynthesis to survive. Excess nitrogen and phosphorus feed blooms, like gasoline on a fire.

Toxic red tide has choked areas such as Charlotte Harbor and Tampa Bay, leaving untold numbers of fish, dolphins and manatees dead. Gray, rotting carcasses wash up on white-sand beaches and beneath the docks of waterfront mansions.

In recent years, the Times identified sharp seagrass losses across major Southwest Florida estuaries that are surrounded by sprawling cities from Clearwater to Fort Myers. They totaled more than 22,000 acres between 2014 and 2022 — including in Tampa and Sarasota bays, which serve as nurseries for fish and grazing grounds for manatees.

Losses touched North Florida, too. Around the sparsely populated Big Bend, where the Suwannee River discharges to the Gulf of Mexico, state scientists identified more than 32,000 acres of seagrass that disappeared over a similar period.

Animated gif shows 89,000 acres of seagrass have died
Tampa Bay Times
Aya Diab

Nowhere has suffered more than the Lagoon.

The waterway’s downfall accelerated with a superbloom of green and blue-green algae in 2011. It gripped the northern reaches, spreading over an area roughly the size of the cities of Tampa, St. Petersburg and Clearwater combined. The algae were small — more than 200 of them could fit on the tip of a mechanical pencil — but together they covered the water like a window shade.

About 34,000 acres of seagrass disappeared from 2009 to 2011, St. Johns River Water Management District data shows.

Around the same time, phosphorus climbed to heights not seen for at least a decade in the northern Lagoon, while nitrogen remained well above healthy concentrations.

The next year brought brown tide, a bloom previously seen in Texas but never in the Lagoon. Scientists still aren’t sure how it reached Florida’s East Coast. Algae again shadowed seagrass beds.

 Blue-green algae surrounds three boats docked in a river
Greg Lovett/Palm Beach Post
/
via AP (2016)
Blue-green algae surrounds boats docked along the St. Lucie River in Stuart. Blooms harm the economy and kill off scores of marine life.
Aerial image shows an algae bloom near homes
Greg Lovett/Palm Beach Post
/
via AP (2016)
An aerial image shows a devastating algae bloom that reached close to homes.

Manatees ate more seaweed in response to the dwindling seagrass. Many were unaccustomed to the new mix of food, and bacteria inside their guts released lethal toxins as a result. From the outside, the animals looked healthy. But the toxins killed them almost instantly.

More than 100 manatees may have died this way in 2013 alone, according to research led by Florida Fish and Wildlife Conservation Commission scientists.

The Lagoon hadn’t even reached the bottom of its freefall.

After the region experienced a short period without severe blooms, about 13,000 acres of seagrass returned by 2015, according to water management district data. But nitrogen and phosphorus levels remained above healthy targets in the northern Lagoon.

Brown tide came back in force the following year, tinting parts of the waterway the color of mud. Oxygen levels in the water plummeted. Countless fish died. The hardest-hit canals and coves were paved with carcasses.

Vast meadows of seagrass gave way to underwater moonscapes. Most ravaged were the areas near dense Brevard: the Banana River Lagoon as well as the northern and central Indian River Lagoon, where phosphorus levels were regularly high.

More than 60,000 acres of seagrass vanished overall between 2007 and 2021, or three-quarters of the previous footprint.

Seagrass has disappeared across Florida. Nowhere suffered more than the Lagoon
More than 60,000 acres of seagrass vanished overall between 2007 and 2021.

Map shows where seagrass disappeared along Florida's east coast
Shreya Vuttaluru/Tampa Bay Times
/
Times analysis of water management district data

For manatees, which can devour about 100 pounds of plants a day, the toll was even worse. Where seagrass held on, shoots became more sparse — leaving them with hardly any food. At the time, estimates suggest, as much as 98% of the seagrass that manatees could have grazed upon was gone.

Scientists theorize the spark that ignited the Lagoon’s downfall more than a decade earlier was a combination of extreme weather — deep cold, then heat. Those conditions stressed an already overburdened environment.

Rafts of fish and seaweed died. As they rotted, they released nitrogen and phosphorus into the water. Smaller, more vexing algae gobbled up the remnants.

Over time, pollution chipped away at the Lagoon’s strength, and when natural challenges such as severe cold hit, the waterway couldn’t bounce back, said Charles Jacoby, a former St. Johns River Water Management District environmental scientist.

“There wasn’t enough resilience,” he said.

The Lagoon bottomed out in late 2020 and early 2021.

That winter, hundreds of manatees retreated to the Florida Power & Light plant in Brevard, where they’d long found shelter.

Drone photo of a power plant
Luis Santana
/
Tampa Bay Times
A drone picture shows the Cape Canaveral Next Generation Clean Energy Center, a reliable source of warm water for manatees in the Indian River Lagoon. The animals gather by the plant to avoid dangerous cold during the winter.

Scientists say young animals seem to learn of such sanctuaries from their mothers. For the rest of their lives, they keep going back, trusting they’ll be safe.

But in the wasted Lagoon, they confronted a dire choice.

They could flee the power plant and risk dying of cold. Or they could stick close to it and chance hunger.

Researchers examine several dead manatees on the sand
FWC
/
Florida Fish and Wildlife Conservation Commission
Researchers examine several dead manatees during the starvation die-off in the Indian River Lagoon. So many animals died that scientists struggled to keep up with the carcasses.

'A 5-alarm fire'

As dozens of dead manatees piled up on the shores of the Indian River Lagoon, Florida scientists were horrified. But they weren’t surprised.

“What I have dreaded for several years is finally being realized,” Charles Deutsch, a veteran Fish and Wildlife Conservation Commission researcher, wrote in an email to colleagues in early February 2021.

To get an unfiltered window into the state’s response to the crisis, the Times reviewed more than 7,000 internal emails from staffers within the agency.

In 2019, a trio of researchers from the conservation commission contributed to a letter in the journal Science, warning that the Lagoon was in trouble. They wrote that decades of regulation and restoration attempts had failed to keep the waterway safe from pollution. Seagrass was declining. They expected conditions to worsen. Manatees were among the many animals at risk.

An emaciated manatee on a blue tarp
Courtesy of FWC
/
Florida Fish and Wildlife Conservation Commission
A Florida Fish and Wildlife Conservation Commission photo shows an emaciated manatee. One sign of starvation in manatees during the die-off was a sunken, peanut-shaped head.
Man in a brown hat recovering a dead manatee in the water
Florida Fish and Wildlife Conservation Commission
Another photo from the agency shows an officer recovering a dead manatee during the starvation die-off. Dozens of carcasses washed up in Brevard County in early 2021.

Deaths started to tick up in late 2020. Between December and January, researchers counted 208 carcasses on the East Coast — many around Brevard.

In early February, Martine de Wit, a veterinarian who studies manatees for the conservation commission, felt certain the animals were starving. Unloading carcasses at her lab, she discovered how emaciated they’d become.

“I immediately sank into the bodies,” she wrote in an email. “They are just like empty bags.”

The conservation commission soon petitioned the federal government to declare an “unusual mortality event,” a bureaucratic term that acknowledged the die-off was an emergency, in need of urgent investigation.

With the public, agency officials shared generic, cautious statements. They said their inquiry was ongoing. But internally, the emails show, researchers were frank, pushing their agency to be more direct.

“It’s not like we’re trying to hide anything!” Deutsch wrote in one message. “We should be doing just the opposite — notifying the world that we have a 5-alarm fire here.”

When de Wit and other staffers cut into dead manatees during necropsies, the carcasses dripped fluid, a sign that the animals’ depleted bodies had essentially started to feed on themselves. Sometimes, their lungs contained seawater, meaning that in their last, exhausted moments, they may have drowned.

One 10-foot manatee de Wit came across should have been huge.

“Almost nothing is left of her,” she wrote to her coworkers.

By spring 2021, more than 600 manatees were dead across Florida. About 250 of them came from Brevard alone.

Many had died from hunger. Others likely grew frail before succumbing to causes like cold stress and boat strikes. Some were known to scientists from past research.

One dead manatee named Megawatt, previously tracked sheltering in the Lagoon, weighed 250 pounds less than she had seven years earlier. There was sand in her gut.

Another, named Heike, first spotted near an old power plant on the Lagoon in 1980, washed up behind a home in Cocoa. Scientists left her remains at the county dump.

Talon, named for a scar by her tail and once tracked swimming as far north as Georgia, died off Titusville. Her muscles and fat had started to liquefy.

“Sorry we lost her too ☹,” de Wit told colleagues by email.

A dead manatee on a concrete floor
Florida Fish and Wildlife Conservation Commission
A Florida Fish and Wildlife Conservation Commission photo shows a dead manatee awaiting examination in an agency lab. Manatees that starved often bore common signs of their suffering: ribs visible through sagging skin, deformed heads, round bellies gone flat.

Other manatees had been known to researchers only by tracking numbers.

They found the emaciated carcass of BC715 on a day when 10 manatees were reported dead in Brevard alone. BC618’s belly skin was so saggy it bunched into folds. R11535 had been spotted in distress but disappeared before rescuers could pluck her from the Lagoon. Two and a half weeks later, she was dead.

Art image says An Estuary In Crisis
Lisa Merklin
/
Tampa Bay Times
Florida has a widespread problem with pollution that happens every time it rains. Click to view a PDF of the path contamination takes from land to water.

At its midway point, 2021 was already the worst year for the species on record. More than 830 manatees had died.

Andy Stamper, a veterinarian at Disney consulted by state scientists about manatee health, vented frustrations to Deutsch. He lamented that conditions in the Lagoon had gotten so dire.

“I just find the whole thing dumbfounding that we are at this state of affairs,” he wrote.

Deutsch bemoaned “conservation by crisis.”

“We need to get the patient out of ER/ICU and back practicing preventative medicine,” he wrote. “Like a slow-moving hurricane, we’ve watched this catastrophe slowly develop over the past decade.”

Scientists desperately looked for ways to help manatees survive another winter. They gathered experts to debate whether they should try feeding animals in the wild.

Considering only health, the researchers asked, would the potential benefits outweigh the risks?

Nearly everyone said yes.

Wildlife officials tossed thousands of pounds of lettuce into the water next to the power plant as hungry manatees gathered. They knew the experiment wasn’t a solution.

Close-up of manatees eating lettuce in the water
Patrick Dove
/
TC Palm (2022)
Manatees eat lettuce thrown to them as part of a government feeding effort amid the starvation die-off.

Just before the unprecedented feeding trial commenced, a supervisor at the U.S. Fish and Wildlife Service shared a draft memo in an email to state officials. It called the die-off the “consequence of a human-caused degradation.”

Feeding manatees would not resolve the problem, the memo stated. “Restoring water quality and healthy seagrass will.”

It was a key message, clearly distilled, that government scientists had returned to for months: The true way to save manatees was to save the Lagoon.

By the time 2021 came to a close, 1,100 Florida manatees were gone.

Manatees swimming in the water
Douglas R. Clifford
/
Tampa Bay Times
The orphaned manatee rescued from the Lagoon in 2021, since named Ashley, swims in a pool at SeaWorld Orlando with other rehabbing manatees.

The fraught path to survival

A fraction of ailing manatees were saved. Along the Atlantic Coast, wildlife officials rescued more than 140 from the beginning of the die-off until late spring 2023. At least half were believed to be starving, some with bones showing through their wrinkled skin.

Sometimes, babies turned up next to the bodies of emaciated mothers, the adults apparently drained from trying to provide for two with limited food. More than 30 of the rescued manatees were calves.

The survivors were rushed to rehab centers across the state. Most were released within a few years. But not all.

Until recently, an orphaned manatee still drifted in a curved pool at SeaWorld Orlando, cradling hunks of lettuce between her flippers. She was the baby biologists found next to the dead mother in January 2021, when the die-off had just begun.

Animated gif of a manatee in blue water shows it stayed in a rescue center for 1,479 days

They’d watched as she swam around the remains, nuzzling close, trying to get milk from the carcass. With little time, the scientists orchestrated a quick rescue.

As daylight faded, they scooped her from the Lagoon using a big net, loaded her into a truck and raced her to SeaWorld. She weighed 115 pounds. For four years, rehabbers kept her safe by tending to her many miles from the damaged waters where she was meant to be — a living reminder that the path out of catastrophe is long.

A young manatee eating lettuce in the water
Douglas R. Clifford
/
Tampa Bay Times
Ashley, a young manatee rescued from the Indian River Lagoon during the starvation die-off, munches on romaine lettuce inside an exhibit at SeaWorld Orlando.
A young boy looking through a glass watching manatees swim at an aquarium
Douglas R. Clifford
/
Tampa Bay Times
A boy admires rescued manatees housed in a SeaWorld Orlando exhibit.

The manatee should have spent her first years at her mother’s hip, floating like a sidecar, learning to live. Instead, caretakers moved her between pools, then to a zoo in Ohio to free up space as the die-off raged, then back to Orlando.

They fed her with a tube until she started eating on her own. They watched her weight closely, tracking each new pound.

At her pool, visitors pressed against a window, ogling the manatees swimming inside without always understanding the calamities that brought the animals there.

Rehabbers dumped box after box of romaine lettuce into the water. The young manatee’s next meal was never in question.

But her future is.

The success of surviving manatees hinges on the health of the waters they return to.

“They're incredibly resilient animals,” said James “Buddy” Powell, a longtime manatee researcher and executive director of the Clearwater Marine Aquarium Research Institute. “If you give manatees half a chance, they're going to survive.”

The orphan’s case holds special promise: One day, she could become a mother herself, helping to propel her species forward.

Wildlife officials prefer to release young manatees like her on cold days, so the animals swim into a crowd of adults and learn of a warm place to shelter for winters to come. The baby was too small to go out on her own — until this year.

As frigid air settled over Florida, the rehabbers made plans to return her to the wild.

But not to the Lagoon.

After several deadly seasons, state officials said conditions in the waterway have started to improve. Still, any progress is fragile.

The area has gone a few years without severe algae blooms, which could be a stretch of good luck following years of bad. Seagrass has made modest returns in some places — though not most. Scientists have stopped feeding manatees lettuce. They’re no longer seeing the animals starve.

Close-up of a manatee's face lying on a blue tarp
Douglas R. Clifford
/
Tampa Bay Times
The orphaned manatee rescued from the Indian River Lagoon in January 2021 arrives at Blue Spring State Park, where rehabbers and volunteers released her to the wild.
A manatee on a blue tarp is measured by two people
Douglas R. Clifford
/
Tampa Bay Times
Before carrying the orphaned manatee to the water, rehabbers measured her and affixed a tracking device to her tail.

Experts warn that celebration would be naive. The Lagoon has seen periods of recovery without algae outbreaks before, only to have a bad bloom trigger another downward spiral. The root of the problem, after all, remains unresolved: Pollution levels are still too high.

In mid-February, the orphan’s caretakers loaded her into the back of a box truck and drove her from SeaWorld to a different manatee haven — a spring in Orange City, nearly 30 miles from the coast.

The water sat still like a looking glass. The sky was bright. Rehabbers and volunteers pulled the manatee — now 890 pounds — out of the truck using a stretcher.

On the ground, they attached a tracking device to her tail. Counting to three, they lifted the stretcher and shuffled down a set of stairs to the water, coaxing the manatee as they went.

“OK, sweet girl.”

“I don’t want to see you again, baby.”

“There you go, sweetheart.”

They lowered her, so the shallow water lapped at her face.

Then, they gave her a nudge toward the blue and let go.

This story is part of the Pulitzer Center's nationwide Connected Coastlines reporting initiative. For more information, go to pulitzercenter.org/connected-coastlines.

This story was originally published by the Tampa Bay Times and shared in partnership with the Florida Climate Reporting Network, a multi-newsroom initiative founded by the Miami Herald, the Sun-Sentinel, The Palm Beach Post, the Orlando Sentinel, WLRN Public Media and the Tampa Bay Times.

You Count on Us, We Count on You: Donate to WUSF to support free, accessible journalism for yourself and the community.