Federal Judge Orders Florida to Address Pollution That Led to Manatee Deaths

The state of Florida is in violation of the Endangered Species Act and must develop a plan for addressing the pollution that led in recent years to an unprecedented die-off of manatees, a federal judge has ruled.

The litigation is centered on state wastewater discharge regulations that have failed to control nutrient pollution in the Indian River Lagoon, a 156-mile estuary on Florida’s east coast that is among the most biodiverse on the continent. The pollution has led to ongoing water quality problems and seagrass losses in this crucial manatee habitat that in 2021 and 2022 left the beloved sea cows starving. Nearly 2,000 manatees died in Florida in that period, a two-year record.

Conservation groups said the deaths represented more than 20 percent of the state’s population. The calamity prompted the U.S. Fish and Wildlife Service and Florida Fish and Wildlife Conservation Commission to resort to providing supplemental lettuce for the emaciated manatees in the lagoon. Each animal requires some 70 pounds of seagrass daily.

Manatees are listed under the Endangered Species Act as threatened. The litigation, brought by the conservation group Bear Warriors United, accuses the Florida Department of Environmental Protection (FDEP) of unlawfully “taking” manatees under the law by promulgating wastewater discharge regulations that have allowed flows from wastewater treatment plants and septic tanks into the Indian River Lagoon (IRL) to continue. These discharges are responsible for the nutrient pollution at the heart of the manatee die-off, according to the litigation.

“As Defendant’s witnesses testified, FDEP is taking important, necessary steps to remediate the polluted waters of the IRL. But that is not enough,” Judge Carlos Mendoza, a U.S. District Court judge for the Middle District of Florida, wrote in an April 11 order. “The North IRL is in such a deteriorated state that the required remediation will take many years, as the state itself has acknowledged. And during that remediation, wastewater discharged pursuant to the FDEP’s regulations will continue to indirectly take manatees in the North IRL.”

Mendoza ordered the state Department of Environmental Protection to obtain what is called an incidental take permit under the Endangered Species Act, which allows animal deaths when they are associated with otherwise lawful activity. The U.S. Fish and Wildlife Service issues the permit after the submission and approval of a Habitat Conservation Plan aimed at mitigating the deaths. 

The Department of Environmental Protection told Inside Climate News in a statement that it disagreed with the ruling and was considering next steps. The department said the state had put nearly $747 million in recent years toward projects designed to remove 2.3 million pounds of nitrogen and 418,000 pounds of phosphorus annually in the Indian River Lagoon region.

“While the Unusual Manatee Mortality Event from 2020-2022 was undeniably tragic, the state of Florida has responded with unprecedented investments to improve water quality and restore habitats, especially in critical ecosystems like the Indian River Lagoon,” the statement from the department reads.

“The facts and outcomes speak for themselves: Between 2021 and 2023, the Indian River Lagoon experienced the regrowth of more than 5,000 net acres of seagrass. Additionally, the U.S. Fish and Wildlife Service recently declared the official closure of the Unusual Manatee Mortality Event, specifically recognizing the historic investments made under this administration,” the statement continued. “DEP remains committed to advancing science-based solutions and continuing to improve Florida’s waterways for generations to come.”

Other estimates for restoring the Indian River Lagoon put the cost at $6 billion, said Pat Rose, executive director of the Save the Manatee Club. He compared the legal action with litigation the federal government pursued against the state some 35 years ago, over water quality problems in the Everglades. That litigation helped lead to a historic restoration effort in the river of grass. Saving the Indian River Lagoon, which spans seven counties and accounts for an economic impact of roughly $7.6 billion annually, would require an effort on a similar scale, he said.

“That’s what it’s going to take,” said Rose, whose organization is involved in separate litigation over nutrient pollution in the Indian River Lagoon against the federal Environmental Protection Agency. “This has to be a major restoration program, [in] which the state of Florida works in tandem with the federal government in order to restore that ecosystem.”

Ragan Whitlock, staff attorney at the Center for Biological Diversity, was heartened by the ruling but said it was too soon to guess what kind of relief it might bring manatees. He said the Trump administration’s proposal this week that would rescind habitat protections for certain species listed under the Endangered Species Act would not affect this particular case.

“We hope it’s a wake up call to the state of Florida that more has to be done to protect waterways and the species that depend on them,” said Whitlock, whose organization specializes in litigation under the Endangered Species Act. “Nutrient inundation into the Indian River Lagoon has to be mitigated to protect not just the Florida manatee but all the waterways and all species.”

The ruling came after a two-day trial in mid-March in Orlando, where Bear Warriors United presented evidence that as much as 99 percent of the seagrass in the Indian River Lagoon has vanished over the last half-century. The problems also have led to breeding problems. Between 2020 and 2022 almost no live manatee calves were observed in the lagoon. It will take at least a decade before the lagoon starts to experience recovery, according to the testimony.

The Unusual Mortality Event designation, declared in 2021 near the start of the manatee die-off, was administratively closed days before the trial began. The U.S. Fish and Wildlife Service and Florida Fish and Wildlife Conservation Commission said researchers had not documented a manatee death linked to starvation and lack of forage for two years.

“We hope it’s a wake up call to the state of Florida that more has to be done to protect waterways and the species that depend on them.”

— Ragan Whitlock, Center for Biological Diversity

Meanwhile the Fish and Wildlife Service proposed in January that the Florida manatee should retain its status under the Endangered Species Act as threatened, despite widespread outcry over the animal’s downlisting in 2017 from endangered. The federal agency said the Florida manatee’s population had stabilized at between 8,350 and 11,730 animals, although the proposal called for the Antillean manatee, a separate subspecies, to be listed as endangered.

Katrina Shadix, executive director of Bear Warriors United, said her group brought the lawsuit after expanding its focus from a controversial bear hunt a decade ago to the widespread habitat loss affecting wildlife statewide. She grew up near the Indian River Lagoon and remembers the lush seagrass meadows that nourished manatees. She paid for the litigation in part with settlement money she obtained after a couple of car wrecks and cried over the ruling.

“I hope this spurs people all over the country to keep fighting the good fight. When you have the morals and the ethics and the selflessness and the altruistic feelings to save something that should never thank you and doesn’t even know that they’re about to go extinct. When you can stand up and fight strong like that, it really is just something that you do to make your kids proud. … It’s just such a good feeling to know that I was a part of preventing manatee extinctions and cleaning up our waters in the state of Florida,” she said, her voice cracking.

“We want everyone to know there are so many people in Florida that care about nature and that care about wildlife and care about our water and land,” she continued. “This win is for everyone in Florida that loves nature.”  

This story has been updated to include information about President Trump’s proposed adjustment of the Endangered Species Act and its impact on manatees.