The Indian River Lagoon saw a brief respite from massive algal blooms this year. But heavy rains from Hurricane Ian led to wastewater spills and stormwater outflows in yet another setback to water quality. Even so, natural resource managers say the lagoon's restoration is still attainable.

This story was funded by the Delores Barr Weaver Legacy Fund at The Community Foundation for Northeast Florida.

In the Indian River Lagoon of 20 years ago, Capt. Billy Rotne could hook a spotted seatrout on cast after cast. Lush seagrass meadows teemed with schools of fish, among them world-record-sized seatrout and bull redfish upwards of 50 inches, making the lagoon a top destination for anglers.

But today, the lagoon’s seatrout numbers are 90 to 95% below historic levels, Rotne estimated. The species, an indicator of water quality, has dwindled in the wake of a decade-long series of severe algal blooms. 

Nutrient pollutants in wastewater and stormwater supercharge these blooms, which block sunlight from reaching seagrass, killing fish habitat. About 75% of the lagoon’s seagrass acreage has vanished since 2011, with a near-total loss in some areas, experts say. 

Seagrasses are ecosystem engineers, organisms that radically shape their surroundings. They anchor the seafloor, slow wave action, store carbon, and house other organisms. A single acre of seagrass can support 50 million invertebrates and 40,000 fish. 

Capt. Billy Rotne holds a spotted seatrout caught in the Mosquito Lagoon, a portion of the Indian River Lagoon, when it was healthier. Now, Rotne says trout are so scarce he no longer targets them. Photo courtesy of Capt. Billy Rotne

“It’s just been a real tragedy to see the loss of the seagrass, the loss of the water clarity, and the subsequent loss of the fish,” Rotne said.

The lagoon’s ailments shot into the national spotlight amid 2021’s record 1,101 manatee deaths. Many manatees starved in the absence of seagrass, their dietary staple.

This year has seen a brief respite from the massive blooms that have come to characterize the Indian River Lagoon, a system of three lagoons that stretches along 156 miles of Florida’s Atlantic Coast. Drier conditions have tempered nutrient-carrying runoff, keeping blooms small, patchy, and short-lived. 

With improved water clarity, some seagrass has returned. It’s a hopeful sign, but these gains could easily disappear, Rotne said.

“It’s a little too hasty to go, ‘Oh, the glory days of the lagoon are back,’” Rotne said. “It’s important that everybody remembers that just because we see some seagrass returning, just because we see moderate improvements, that the lagoon is still very fragile.”

We’re about halfway home.

Chuck Jacoby, St. Johns River Water Management District

Some of the lagoon’s recent rebound may have been erased as Hurricane Ian delivered up to 21 inches of rain to parts of coastal Central Florida. The deluge sent nutrients coursing to the lagoon and triggered wastewater spills and stormwater overflows. Fishing the Vero Beach area in the weeks following the storm, Capt. Paul Fafeita saw that once-clear water had been replaced with what looked like chocolate milk.

“It actually smelled like raw sewage in some areas,” Fafeita said.

Ian offered a grim reminder that the Indian River Lagoon’s route to recovery will continue to be long, difficult, and expensive. Scientists estimate seagrass could take 12 to 17 years to regain its previous foothold, even under the best circumstances. 

Capt. Rocky Van Hoose, the author’s father, wade-fishes the shallow waters of the Banana River in August 2021. It’s one of three lagoons that make up the Indian River Lagoon system, along with the Mosquito Lagoon and the Indian River. Before the cycle of massive algal blooms that began in 2011, water in the lagoons was clear for most of the year. Photo courtesy of Natalie van Hoose

But natural resource managers working to slow the influx of algae-feeding nutrients, such as nitrogen and phosphorus, say restoration remains attainable.

The take-home message is “stay the course,” Chuck Jacoby, an environmental scientist with the St. Johns River Water Management District, said at the Indian River Lagoon Research Symposium in April. “We’re about halfway home.”

 A Microscopic Coup

The Indian River Lagoon stretches along 156 miles of Florida’s Atlantic Coast. Water can take weeks to years to flush out of certain parts of the lagoon, and because it lacks an upstream and downstream, improvements made in one part of the lagoon don’t always trigger recovery in others. Image courtesy of Marine Resources Council IRL Health Report Card

Historically, seagrasses were the Indian River Lagoon’s foundational organisms, powering what was once North America’s most biodiverse estuary. But in 2011, another group of life forms began to define how the waterway worked. 

That March, out-of-control numbers of two types of algae combined to create a “superbloom” that spanned an estimated 132,500 acres across the lagoon – larger than the footprint of the city of Tampa. Concentrations of chlorophyll-a, a pigment that scientists use to measure bloom intensity, were eight times above average in some areas. The bloom lasted for seven months.

Blooms are a normal part of the lagoon’s cycle, but not at this magnitude.

“In vast areas, there wasn’t a lot of light getting down to the bottom for seagrasses to survive,” said Ed Phlips, an expert in algal biology and ecology at the University of Florida. Phlips has been studying the Indian River Lagoon since 1997. Still, the scale and duration of the 2011 bloom took him by surprise. “I realized at that point, I didn’t really understand the system as well as I thought.”

The superbloom was followed by others even more severe. Without enough sunlight, the lagoon’s 80,000 acres of seagrass gradually shrank to about 20,000, according to a 2021 survey by SJRWMD.

In 2021, Phlips and his collaborators published a study based on 23 years’ worth of data on the lagoon’s water quality, light levels, nutrient levels, water circulation, and other properties – a full body scan of its health. The data tell a story of two starkly different lagoons: one before 2011 and one afterwards. 2011 ushered in what the scientists call a “regime shift,” a dramatic change in the ecosystem’s structure and function.

This image shows the loss of grass between the St. Johns River Water Management District’s 2019 and 2021 surveys in Brevard County. SJRWMD estimated the lagoon housed 33,205 acres in 2019, which dropped to 19,821 last year. Image courtesy of the St. Johns River Water Management District

Algae play a key role in the lagoon’s food web, and before 2011, researchers had mapped a cyclical pattern of blooms typically appearing in summer and amplified by heavier rainfall, such as in El Niño years.

These new blooms, however, are far more frequent, intense, and longer-lasting than those of the past. They also tend to be dominated by a different set of algal species. Many of these species are smaller than their predecessors, allowing them to reproduce faster. And some, including the algae that causes the phenomenon known as “brown tide,” have a coating that provides a natural defense against would-be predators, making them harder to control, Jacoby said.

Some of these new bloom-dominators are also more cold-tolerant, leading to a broadening of bloom seasonality. Now, blooms can break out in winter and spring, overlapping with the peak period of growth for seagrass. The warmer temperatures brought by climate change also prolong blooms’ growing season.

“Until this last year and a half, we were typically facing blooms almost every year,” Phlips said. “That meant it was impossible for seagrass to recover.”

A Long, Slow Build-Up

The Indian River Lagoon’s water quality crisis is not the result of a sudden shift in the system, but the culmination of a long, slow build-up. Coastal development along the lagoon has been consistent since the 1950s. For decades, the state’s infrastructure has provided pathways for nutrients from wastewater treatment plants, septic tanks, landscape fertilizers, and agricultural operations to speed into the lagoon.

Natural resource managers had nutrient pollutants on their radar by the 1990s, long before the 2011 superbloom. In response, they developed plans to reduce flows of nitrogen and phosphorus to the lagoon. But decades of what managers call “legacy loading” had built up in the waterway over time, priming it for collapse when stressed.

Blue-green algae grow quickly when fueled by nutrient pollutants such as nitrogen and phosphorus, common components of plant fertilizer. These algae can produce a toxin that sickens people and animals, contaminates drinking water, and can lead to closures of boating and swimming sites. Photo courtesy of Duane De Freese, Indian River Lagoon Council

Initially, the 2011 superbloom may have been triggered by natural causes, including the unusual cold of the previous two winters, Phlips said.

Water temperatures then dropped to about 40 degrees Fahrenheit, roughly 20 degrees below their typical low. Fish, seagrass, and drifting macroalgae began to die, releasing nutrients as they decomposed. As the water warmed, muck on the lagoon bed – the product of legacy loading – released additional nitrogen and phosphorus.

In the absence of competitors, tiny algae could feast on this sudden surge of nutrients and multiply unchecked.

Pyrodinium bahamense commonly causes toxic algae blooms in the Indian River Lagoon. It prefers warmer temperatures and has historically bloomed in the summer. With climate change, blooms are beginning earlier in the spring and lasting later into the fall.  Photo courtesy of Malcolm McFarland, FAU-Harbor Branch Oceanographic Institute

Under normal circumstances, the lagoon may have been able to rebound from such a bloom on its own. But its diminished health locked it into a negative feedback loop. Without the anchoring support of seagrass, sediments swirled freely in the water, making it more difficult for grass to re-establish a foothold.

“[Algae] have always been important,” Phlips said, “but now they’re taking up most of the light and most of the nutrients.”

‘Slowing the Loading’

Natural resource managers are taking a region-wide, multipronged approach to reduce nutrient levels in the lagoon. Brevard County’s Save Our Indian River Lagoon program is estimated to bring in up to $489 million over 10 years to fund projects to reduce or remove about 1.3 million pounds of nitrogen and 105,000 pounds of phosphorus annually. The funding comes from a half-cent county sales tax that started in 2016.

These projects include dredging muck, upgrading septic tanks and connecting them to sewage systems, repairing leaks in pipelines, and slowing the flow of stormwater using techniques such as baffle boxes and permeable pavers. 

During Hurricane Ian, Brevard County released 7.2 million gallons of wastewater into the lagoon. Photo courtesy of Tyler Jones, UF/IFAS

Thus far, completed projects have moved the county 12.5% closer to its targeted nitrogen and phosphorus reductions, said Virginia Barker, director of Brevard County’s natural resources management department.

“We’re 25 to 50% of the way towards getting the water clear enough that we might expect seagrass to be able to survive most years,” Barker said in an email.

Some say it’s not enough. While Rotne applauds the program’s focus on converting septic to sewer, he said Brevard also needs to upgrade its wastewater treatment systems to avoid the spills that can happen when outdated infrastructure faces a surge of rainfall. During Hurricane Ian, the county released 7.2 million gallons of wastewater into the lagoon. 

It’s not just about costs; it’s about value.

Duane De Freese, Indian River Lagoon National Estuary Program

“When they get large influxes of stormwater, the systems are not capable of handling that, and they have to literally release the water,” Rotne said. “Oftentimes these sewage treatment plants are built right on the side of the lagoon.”

Brevard County’s program joins $70 million in state investments dedicated to the lagoon’s health, according to Ashley Evitt, SJRWMD’s media outreach manager. And in 2021, the Army Corps of Engineers debuted a new plan for managing outflowing freshwater from Lake Okeechobee. The plan is projected to divert about 35% of the lake’s nutrient-rich water during the rainy season away from the St. Lucie Estuary and the southern Indian River Lagoon where it causes blue-green algae blooms. Instead, the water will flow south to the Everglades, mimicking its historic pathway.

But restoration will not come cheaply. Speaking at April’s symposium, Duane De Freese, executive director of the Indian River Lagoon National Estuary Program, said resurrecting the lagoon may cost upwards of $5 billion. 

De Freese added, however, that a 2016 economic valuation report by the Treasure Coast Regional Planning Council equated each dollar invested in the lagoon to a return of $33. The lagoon contributes an estimated $7.6 billion to Florida’s economy annually. 

“That’s a good deal,” De Freese said, “and that’s the story we need to tell when we start talking about the cost. It’s not just about costs; it’s about value. If we have resolve, if we have political will, then this is a doable project.”

Jacoby likens reductions in nutrients to putting the Indian River Lagoon on a diet. Restoring salt marshes and filter-feeders, such as oysters and clams, is a form of physical therapy. And monitoring the lagoon’s recovery and adjusting actions as needed is like giving the waterway regular checkups and preventative care.

“The key focus is on slowing the loading,” Jacoby said. “Not all algal blooms are bad. Algal blooms are part of the system. When our actions exacerbate those blooms – make them last longer, make them more intense, make them more widespread – that’s when we have issues.”

Disclosure: Natalie van Hoose previously worked at the University of Florida and has occasionally written for the university as a freelancer.

Natalie van Hoose is a Florida-based freelance science writer who covers water, wildlife, and sustainability. Her work has appeared in Fast Company, Florida Sportsman magazine, WEDU PBS, Cool Green Science, Creative Nonfiction magazine, and other outlets. She grew up in Cocoa Beach.

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

Cover image: The Indian River Lagoon at New Smyrna Beach in July of 2014. Photo courtesy of Tyler Jones, UF/IFAS