The mammals were removed from the endangered species list in 2017, but algae blooms and overdevelopment have killed 46,000 acres of seagrass, leaving manatees without enough to eat.

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In Florida, wildlife managers and environmental groups have been stunned this year by the number of manatee deaths. Manatees are large marine mammals native to Florida, which spend their time grazing on seagrass in shallow coastal areas. NPR's Greg Allen reports that many of the deaths are in Florida's Indian River Lagoon, where a large die-off of seagrass has left manatees without enough to eat.

(SOUNDBITE OF BOAT ENGINE STARTING)

GREG ALLEN, BYLINE: It's a beautiful day on Indian River Lagoon. Biologist Ryan Brushwood starts the engine on his small flatboat to check on seagrass he's planted in the estuary. The water has a slight greenish tint but is clearer than it was in January when, Brushwood says, there were algae blooms.

RYAN BRUSHWOOD: When those blooms were really bad, I mean, you couldn't see your hand below the surface. There was not a lot of light getting down to the plants.

ALLEN: Indian River Lagoon isn't actually a river. It's a large estuary bounded by barrier islands on Florida's Atlantic coast. It extends more than 150 miles from Cape Canaveral to Stuart. For years, there have been concerns about declining water quality in the lagoon, caused by a number of factors, including development, septic systems, stormwater runoff and warming temperatures from climate change. In 2011, an algae superbloom covered more than 130,000 acres of the lagoon's water, blocking the sunlight and causing a massive die-off of seagrass.

BRUSHWOOD: In hindsight, it probably was the tipping point, and there was (ph) many factors that occurred before that.

ALLEN: Manatees love Indian River Lagoon, and for years, it provided them with lush seagrass. That's not the case now. Scientists say there's been a decrease of about 46,000 acres. Indian River Lagoon is a special and fragile place. It's one of the most biodiverse estuaries in the Northern Hemisphere, home to 35 species that are endangered or threatened. Nearly a third of Florida's manatees spend some time in the lagoon each year. But the large die-off of seagrass has left them without enough to eat. Jon Peterson heads rescue operations at SeaWorld. Since December, his crews have been busy responding to the large numbers of sick and dying manatees.

JON PETERSON: It's really eye-awakening when you watch what's going on. You have animals that are out there floating high to what you would - in a normal year, you'd think it's a punctured lung, you know, an issue from a boat strike. And what it's turning out to be is it's a starvation event.

ALLEN: More than 750 manatees have died this year, the most deaths ever in a five-month period. More than half of them were in Indian River Lagoon. The high number of deaths has the U.S. Fish and Wildlife Service concerned, and it's opened an investigation. Peterson says the entire population of manatees in Florida is estimated at no more than 6,800.

PETERSON: When you're talking a population like that and you have a loss of 700 in your first quarter of the year, it is a very scary look right now.

(SOUNDBITE OF WATER SPLASHING)

UNIDENTIFIED PERSON: All right, guys, careful.

ALLEN: Florida Fish and Wildlife Conservation Commission crews this spring responded to more than 90 reports of manatees in distress, including orphaned calves. This one was rescued in May and taken to SeaWorld in Orlando. SeaWorld is one of four facilities in Florida that rehabilitate sick and injured manatees. Peterson says his staff is caring for 28 of them. Ten are so weak they're getting nutrition through feeding tubes. Because the manatees have lost so much weight, he says rehabilitation takes longer than usual.

PETERSON: You're talking an animal that's down, let's say, 400, 500 pounds. It will take us three to five months to put that weight back up there to get them to a point where we can release them.

ALLEN: Manatees don't do well in cold water, which is why they congregate during the winter months in Indian River Lagoon and other Florida coastal areas. Now that it's warming up, scientists say manatees are beginning to disperse to other areas along the Gulf and Atlantic coasts, where they may find ample seagrass. But by late fall, they'll return again in large numbers to familiar waters, including the lagoon. Michael Walsh, an associate professor at the University of Florida who specializes in aquatic animal health, is worried this mortality event may be far from over.

MICHAEL WALSH: We have a compromised system that the animals have to utilize and stay in, but the food is just not there at the same amount that it used to be.

ALLEN: The key to helping manatees, Walsh and other scientists say, is to get the Indian River Lagoon healthy. That will take years, maybe decades. But there are signs of progress. Florida just allocated a half-billion dollars to phase out septic systems, a key contributor to the region's nutrient pollution. And in the lagoon, the company Ryan Brushwood works for, Sea & Shoreline, is having success restoring seagrass.

BRUSHWOOD: You can see there's nine shoots growing off of one single rhizome. It looks pretty healthy. That's kind of the density that we're seeing right now.

ALLEN: Working on a grant from the National Estuary Program, Sea & Shoreline planted two acres of a resilient species of seagrass last June. A year later, it's thriving. Similar replanting efforts helped bring back healthy seagrass beds in Crystal River, another manatee habitat in Florida. Brushwood believes that with enough time and funding, a large-scale effort could bring seagrass back here and tip things back in favor of the manatees.

Greg Allen, NPR News, Cocoa Beach, Fla.

(SOUNDBITE OF COCTEAU TWINS SONG, "PANDORA (FOR CINDY)") Transcript provided by NPR, Copyright NPR.

Tags: Indian River Lagoon  manatees  Florida