FORT PIERCE, Fla. -

There’s a deadly mystery hidden in the murky waters of a once vibrant South Florida lagoon.

Bottlenose dolphins and endangered manatees are dying in record numbers in Indian River Lagoon, a coastal body of water separated from the ocean by barrier islands. Its brackish waters stretch along 156 miles of coast from Hobe Sound near West Palm Beach north to the Kennedy Space Center.

While some researchers have their guesses, no one really knows exactly what’s behind the deaths. Brian Lapointe, a researcher at the Harbor Branch Oceanographic Institute at Florida Atlantic University, called the deaths of more than 60 dolphins and 100 manatees since the beginning of the year a "tipping point."

Fellow researcher Adam Schaefer studies the various diseases that plague the lagoon’s dolphin population.

“Because marine mammals are at the top of the food chain, they tend to kind of reflect all of the things happening beneath them,” he said.

Watch: Schaefer on dolphin diseases

Schaefer said the dolphin deaths, estimated to be about 10 percent of the total lagoon population and the largest the estuary has ever experienced, are happening in the northern portion of the lagoon. Lapointe said with fewer inlets to the Atlantic Ocean, toxins linger longer there.

“There have been so many deaths that the National Marine Fisheries have declared it an unusual mortality event,” he added.

According to the National Oceanic and Atmospheric Administration (NOAA): “Current bottlenose dolphin strandings are almost three times the historical average for the Indian River Lagoon. All age classes of bottlenose dolphins are involved, but the majority of animals are older adults and a few juveniles.”

"Right now, it's not clear what the actual cause of death is," said Schaefer.

NOAA has since created a task force to investigate the deaths.

Schaefer said the dolphins act as a barometer to the rest of the environment.

"The big canary in the coal mine concept where what we see in this species of population could tell us what is happening in the environment," he said.

Troubled ecosystem

Lapointe believes the deaths mean the lagoon's ecosystem is in trouble. He monitors the manatees and what they eat.

Sea grass is the manatees’ primary food source and several varieties have been steadily dying due to the emergence of large algae blooms in recent years.

“What happens is this reduces the amount of light penetrating to the bottom that the sea grasses need to grow," he said. "Once you have these blooms, you have inadequate light to support your sea grasses and they die off.”

Watch: Lapointe on manatee deaths

Lapointe has found the marine mammals are now turning to a red sea weed known as Gracilaria as an alternative food source, an algae that has become toxic and is thriving in an ecosystem dangerously out of balance.

“The nitrogen to phosphorus ratio in the water and the algae is very, very high,” he explained, which is why the algae is toxic to the manatees consuming it.

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Published On: Oct 02 2013 02:42:08 PM EDT
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Contributing factors include watershed rain run-off and discharges from Lake Okeechobee. The fresh water surges into the lagoon darkens the water and lowers salinity levels.

But Lapointe said like the dolphins, the manatees are dying in the north where “only a very small amount of nutrients from Lake Okeechobee would get up there.”

Lapointe also found the source of the area's high nitrogen levels: septic tanks.

“These algae blooms that we are seeing are being supported by sewage nitrogen not fertilizer nitrogen," he said.

Lapointe added that there's likely other sources playing a role in the wildlife mortalities “many of which are likely producing toxins that we don't know about yet."

"We swim in these waters, we recreate in these waters and many of us consume fish or shellfish out of these waters," he said. "We need to look more broadly at other toxins that we don't know about. That’s very expensive research it really needs to be funded on a fast track.”

“We are at the point where we need a lot more research,” said Schaefer. “What I am interested in is what it can tell us about the potential risk to human health.”

Lapointe wants lawmakers to increase research funding and support the creation of models to improve the management of a lagoon in crisis.