Bioluminescent algae on Florida’s East Coast are part of increasing numbers of algae blooms in the U.S. — some of which are toxic, with possible impacts including tainted drinking water and poisoned shellfish beds. (Florida Today Communications/PR Newswire)

Karen McLaughlin normally carries a flashlight for her nighttime kayak trips along Florida’s Banana River to spot any alligators resting on the banks. But these days, it’s the river itself that glows in the dark.

“It’s beautiful!” McLaughlin, an eco-tour guide, said as her boat’s wake set off an eerie light show on a moonless October night. Each dip of her paddle stirred up bioluminescent plankton that have invaded this eastern Florida waterway in record numbers since late summer. Like millions of tiny fireflies, they lit a jumping fish in a geyser of emerald light. A manatee out for the evening glowed like an alien spaceship as it passed underneath.

It was striking, but also strange: In a region where explosive “blooms” of toxic or nuisance algae have battered fisheries and killed dolphins and sea turtles in recent years, the glowing microorganisms represent another mysterious shift in an ecosystem that scientists say is out of kilter.

In the same week that some Florida researchers monitored the bioluminescent algae on Florida’s East Coast, others were keeping watch on remnants of a massive “red tide” in the Gulf of Mexico, a swath of toxic algae that at one point stretched 100 miles.

From Southern California’s beaches to the Chesapeake Bay, waterways across the United States are seeing increasing numbers of algae blooms, with impacts including tainted drinking water and poisoned shellfish beds. Some are linked to higher levels of nitrogen pollution from livestock waste and fertilizers from suburban lawns and farms. Others are mostly natural events that are occurring in new places as oceans and inland lakes grow warmer.

Harmful algal blooms occur when colonies of certain types of algae grow out of control. Certain types of algae produce toxins that enter the food chain through fish and shellfish. (National Ocean Service/NOAA/YouTube)

Local economies at risk

But in Florida, where three-quarters of the state’s 20 million residents live in coastal counties, a sudden change in the water is more than a colorful curiosity. Algae blooms, with their potential for damaging local economies, are the subject of particularly intense research here, as scientists and environmental officials seek to pinpoint their cause while improving early detection systems that can predict when and where they will occur.

While recent discoveries have helped unravel some of the mysteries behind the appearance of algae blooms, they also underscore for local officials and business owners the extreme difficulty of resolving a problem that stems from decades of overdevelopment and lax controls. In Florida, officials are debating solutions including improved wastewater treatment and vacuuming up several feet of organic sludge that lies at the bottom of some coastal waterways.

“People like to point fingers, but all of us are to blame,” said Clark Giangarra, a former Long Island clammer who has operated charter boats for eco-tourists and fishermen for 30 years along Florida’s central Atlantic Coast. “These organisms have existed here forever, but the system goes crazy when you dump in too many nutrients.”

Gigantic red tide

The sheer scale of some of the recent outbreaks strains comprehension. The enormous red tide that developed off the state’s Gulf Coast is one of the largest ever measured: about 6,000 square miles, or slightly larger than Connecticut. Red tides, caused by a species of toxic plankton, are not directly triggered by nutrients from the land, but some scientists believe that red-tide episodes are occurring earlier in the season and lasting longer because of climatic changes that heat up the oceans.

Florida scientists activated sensors and dispatched new underwater robots called “gliders” to explore this year’s red tide and beam signals to monitoring stations on land. The new equipment allowed health officials to “see” the algae bloom as it starts to form, days or weeks before the appearance of telltale swaths of red water on the surface, said Quay Dortch, who heads a program for algae-bloom research at the federal National Oceanic and Atmospheric Administration.

“We have reached the point where we can see it coming,” Dortch said.

While massive in size, this year’s red tide has mostly remained offshore, with only occasional patches washing up along Gulf of Mexico beaches where they can kill fish, poison oyster beds and cause respiratory problems for mammals, including dolphins and people.

By contrast, on Florida’s central Atlantic Coast, algae invasions have tended to be smaller in scale but more disruptive to wildlife and local economies. The Indian River Lagoon, a 150-mile long estuary that runs from Cape Canaveral to just north of Palm Beach and is regarded as one of the country’s most diverse and productive waterways, is recovering from a disastrous “brown tide” algae bloom in 2011. Then, the waterway — which includes numerous smaller tributaries such as the Banana River — became choked with mats of algae so dense that it blocked the sun’s rays from reaching the sea bottom, wiping out sea grasses that serve as a critical food source and nursery for many of the region’s marine species. Manatees, the gentle sea mammals beloved by Floridians, died by the scores from disease and the toxic effects of seaweed and other plants that became the manatees’ alternative diet.

A buildup of changes

The reasons for the destructive outbreak are in dispute, but new research shows that years of seemingly subtle changes — from upticks in water temperature and salinity to a gradual buildup of nutrient-dense sludge on the sea floor — helped set the stage for the drastic changes seen in more recent years.

Today, a single event, such as a hurricane or a sudden temperature change, can trigger a “trophic cascade” in which harmful species can come out on top, said Brian Lapointe, an expert on algae blooms and a professor at Florida Atlantic University’s Harbor Branch Oceanographic Institute.

“When you disrupt the ecosystem with nutrients, it creates a bottom-up effect that goes right up the food chain,” Lapointe said.

The pollutants that cause algae blooms are primarily nitrogen and phosphorus that seep into the water from countless subdivisions, livestock operations and fertilized fields that line the waterways and tributaries farther upstream. It’s the same problem that regional governments have grappled with for years in the Chesapeake Bay, where excess nutrient pollution creates annual “dead zones,” a closely related phenomenon that occurs when decaying algae suck the oxygen from the water. Fish and other aquatic animals that can’t escape from a dead zone die of suffocation.

As in Florida, the problem for the bay is that the farms and cities in the watershed keep growing, replacing forests, wetlands and meadows that once served as a filtering buffer for polluted rainwater runoff, conversation groups say.

“Without this natural filtering system, when it rains, the water washes pollution into our local creeks, creating a toxic stew,” said Hedrick Belin, president of the Potomac River Conservancy, a nonprofit group devoted to the river’s protection.

And the Chesapeake Bay region is hardly alone. Last year, harmful algal blooms were reported in 21 states, up from 20 states the previous year, according to a report by the National Wildlife Federation’s Great Lakes Regional Center, an environmental nonprofit group, and Resource Media, a nonprofit public relations organization. New York reported 50 cases of toxic algae outbreaks, followed by Kansas with 18 and Washington with 12.

An August algal bloom in Lake Erie brought Toledo to its knees, forcing residents to turn off their taps for three days after health officials declared city water to be unsafe to drink. The reason for the bloom was a familiar story: Sewer overflows, farm fertilizers and a cocktail of nutrients from livestock manure created the perfect conditions for algae to bloom in great mats of green slime.

A septic culprit

New science is making it easier to pinpoint precise sources of pollution for specific events. In Florida, a chemical analysis by Lapointe’s laboratory showed that much nitrogen is seeping into the water from tens of thousands of leaking septic tanks, the go-to choice for home builders in a region that lacks sufficient municipal wastewater treatment. For years, developers have opposed new water-treatment plants so they could build houses cheaply and quickly to satisfy the state’s ever-growing demand, Lapointe said.

“Septic tanks have been the magic carpet for the developers in getting communities built quickly,” Lapointe said. “But now it has caught up with us.”

The impact of excessive nutrients can differ from one year to the next. The “brown tide” of 2011 did not return this year, but scientists continue to see dramatic shifts in plankton populations, including this year’s explosive growth of bioluminescent plankton in the lagoon’s upper reaches near Cape Canaveral. The tiny creatures that cause the water to light up are hardly new to the region, and while some emit a mild toxin, they are generally regarded as harmless.

Yet, this year’s bloom was unprecedented in the memories of local scientists and outdoorsmen, said Lapointe, who added that toxins from huge numbers of plankton are starting to concentrate in some fish species. Though striking to look at, the colorful plankton are a symbol of changes with “ramifications up and down the food chain,” he said.

“When you disturb the system with nutrients, you get can get shifts in the frequency and extent of these microbial populations,” he said, “and that can lead to serious negative effects, both for ecosystems and for human health.”

joby.warrick@washpost.com

darryl.fears@washpost.com

Fears reported from Washington.