Site icon Conservation news

Building back Miami’s Biscayne Bay: Do natural solutions hold hope?

  • A massive fish kill in August 2020 was a red flag that historically troubled Biscayne Bay in Miami had passed a biodiversity health tipping point.
  • Years of scattered efforts and mixed results of various conservation actors working toward the bay’s recovery have begun to fade in favor of more collaborative, inclusive efforts.
  • Scientists and citizens are now focusing their efforts on creative ways to restore biodiversity in Biscayne Bay.

MIAMI — Along the Miami shoreline, luxury high-rises and condominiums run parallel to Biscayne Bay, one of South Florida’s most biodiverse ecosystems, characterized by its once abundant coral reefs, seagrass beds and mangroves.

But increasing population pressure, pollution, and the effects of climate change have left the bay in shambles. Reefs are dying, seagrass beds have disappeared, and algal blooms have depleted the bay’s marine life as a result of nutrient pollution and hotter temperatures, leaving organisms starved for oxygen.

Amid the pandemic, though, a tragic “aha! moment” brought a renewed commitment to the bay.  A massive fish kill in August 2020 prompted communities across Miami to amp up their efforts to restore balance to the bay. The work of scientists, activists and city officials in particular has turned toward effectively undoing more than a century of damage to an ecosystem now in haphazard flux.

One of the questions that remains at the fore of the conversation over Biscayne Bay is: Can nature-based solutions bring it back to life?

Two octopi found dead
Two octopi found dead from the August 2020 fish kill. Image courtesy of Miami Waterkeeper.

An ominous warning sign

In August 2020, Miami Beach residents complained of a rotten stench that wafted across the summer air. Fish, rays, eels, lobsters, shrimp, crabs, octopus, and all kinds of other marine life bobbed lifeless on the surface waters of Biscayne Bay.

Scientists familiar with past die-offs sprang into action — this wasn’t Biscayne Bay’s first fish kill — concluding that it was the result of fatally low oxygen levels caused by nutrient overload.

Florida Fish and Wildlife Conservation Commission scientists said the die-off was spurred by a combination of heavy rainfall and hotter-than-usual temperatures in the bay, conditions that could occur again.

A main source of nutrient pollution in Biscayne Bay is sewage waste from poorly maintained septic systems and fertilizer runoff, both of which contribute excess nitrogen and phosphorus that feed excessive algae growth. Miami-Dade county officials have developed an action plan to replace (and finance) septic systems across the area in the face of sea level rise and other climate change impacts. The county has identified 25,000 septic systems, out of the more than 120,000 known to exist, that are currently failing or at risk of doing so, chief bay officer Irela Bagué told Mongabay in an interview.

“The reason why they’re failing is because they’re in low-lying areas,” she said. “They’re already subject to chronic flooding, whether it’s king tide or areas that just flood.”

Rays and pufferfish were among the larger fauna found dead in Biscayne Bay during the August 2020 fish kill. Image courtesy of Dylann Turffs / Miami Waterkeeper.
Dead fish during the August 2020 fish kill. Image courtesy of John Cline.

Suddenly, the environmental threat of septic tanks became real, and when marine life turned up dead in August, people wanted answers.

Miami Waterkeeper, an environmental advocacy NGO, garnered the help of the community to report fish kill sightings and submit photos to the organization as a way to collect data and distribute resources.

“It was really distressing that we could see all of these fish gathering at the surface gasping for air,” Rachel Silverstein, executive director of Miami Waterkeeper, told Mongabay in an interview.

During a late-night brainstorming session, the organization’s team came up with an idea to artificially add oxygen to the bay. They deployed storm water pumps in certain areas to restore oxygen levels in localized pockets of the bay as a last-ditch effort to resuscitate an ecosystem on life support.

Although these oxygenated areas provided some refuge for wildlife, Silverstein notes it was only a short-term solution.

“We certainly don’t ever want to have to do that again,” she said. “If we’re going to invest resources in preventing and addressing water quality issues in the future, we really don’t want to focus too much on aeration because we want to fix the systemic problems leading to these low-oxygen conditions.”

YouTube video player

Scientists had long warned that Biscayne Bay was quickly approaching a tipping point. Decades of research and growing awareness had preceded the August 2020 fish kill, which “really did provide a catalyst to take action,” Silverstein said. “It was now impossible to ignore the water quality issues in Biscayne Bay, and people were seeing the effects that had been warned about through the years coming to fruition.”

Dozens of volunteers helped remove dead fish from the bay, crucially removing decomposing organic matter that could worsen algae blooms, Silverstein said.

“We weren’t sure that people would be willing to come out in the middle of the pandemic in the summer in Miami to clean up dead fish, but we found that they absolutely were that dedicated to keeping our water clean,” she said.

It was an early example of how the tragedy spurred the community to take quicker action.

Blue land crabs (Cardisoma guanhumi) depend on a moist environment to survive, spending part of their lives in the ocean and burrowing in holes on land. Image courtesy of Marlowe Starling.

A century-old problem

Biscayne Bay is tied to a larger watershed with a fateful history.

Prior to human development, according to hydrogeologist Michael Sukop with Florida International University (FIU), the water once traveled as sheet flow from the Everglades to Biscayne Bay.

Miami’s boom in activity and development in the early 20th century saw much of the area’s wetlands dredged, drained and diverted into canals, which were meant to prevent flooding by altering the natural flow of freshwater. Many of the bay’s modern-day challenges, from fish kills to seagrass die-off, are symptoms of this altered flow.

Sukop says that rather than emptying into the bay diffusely, water now empties from 21 distinct basins, releasing concentrated amounts of nutrients. What used to be a subtropical estuary is now an estuarine lagoon in flux, with fluctuating salinity and oxygen levels, limited freshwater circulation and poor water quality.

“To reverse these kinds of intensive, built environments, it’s so almost unimaginably expensive,” Sukop told Mongabay in an interview.

Infrastructure plans that accommodate the state’s growing population continue to place pressure on South Florida’s watershed and are evidence of the state government’s agenda. There are also pending plans to build a highway through wetlands near the Everglades that recharge the Floridan aquifer.

Restoring historic water flow has been a focus of restoration plans for Biscayne Bay and the Everglades. As part of the Biscayne Bay Coastal Wetlands Project, the Deering Estate, a protected area spanning more than 180 hectares (450 acres), has also participated in rehydration projects to restore historic sheet flow to the bay. Deering Estate staff say they have documented the return of several rare and keystone species as a result, including river otters (Lontra canadensis) and diamondback terrapins (Malaclemys terrapin).

But some argue that nature-based solutions hold more substantial promise.

YouTube video player

Mangroves, for example, act as natural barriers to storm surge, helping to dissipate the energy thrust upon the state’s coastlines by hurricanes. Part of the Biscayne Bay Task Force’s plan includes a mangrove restoration and protection program to create “living shorelines” as natural infrastructure.

Still other potential nature-based solutions depend on restored freshwater flow, such as one project aiming to restore oyster beds that would naturally filter out pollutants before they reach the bay.

As local officials and citizens try to develop ways to restore the bay’s health, scientists are bracing for the possibility of another tragedy.

So, where’s the tipping point?

A long history of urban coastal development in South Florida might make it seem as though Biscayne Bay’s problems have been a century in the making. But it is in the most recent decades that nutrient pollution has gotten worse.

“The nutrients story — it’s been bad, and it’s been bad for a long time,” Todd Crowl, director of FIU’s Institute of Environment, told Mongabay in an interview. “It just keeps getting worse, now that the infrastructure is declining so fast.”

Warmer temperatures mixed with high nutrient levels from septic tank leakages and fertilizer runoff — which are exacerbated by heavy rains, flooding, king tides and storm surge — are key ingredients for harmful algal blooms. The phenomenon occurs when excess amounts of nutrients, notably phosphorus and nitrogen, cause algae to grow out of control, which chokes oxygen out of the water. As a result, the rest of the food chain suffers, sometimes leading to large-scale fish kills.

But at the root of the food chain, seagrass is a key component of the Biscayne Bay ecosystem. The aquatic vegetation is home to crustaceans and other invertebrates like sponges and corals, providing food for larger fish and mammals, like Florida manatees (Trichechus manatus latirostris), which are starving to death at an alarming rate this year due to seagrass loss.

Scientists estimate that seagrasses have decreased by up to 90% in some areas of Biscayne Bay and have disappeared entirely from others. That creates a problem for organisms that depend on the vegetation for habitat and food. Additionally, seagrasses extract nitrogen and phosphorus from the water, release oxygen, cycle nutrients, stabilize sediments and store carbon.

A baby manatee (Trichechus manatus) kisses an adult on the cheek at the Deering Estate in Miami, Florida. Image courtesy of Elias Horna.

The ecosystem still hasn’t recovered from a major seagrass die-off from two decades ago, Crowl said. He explained that Biscayne Bay was once seagrass-dominated before it was dredged, deepened and filled with sediment from heavy construction. This led to a shady environment that doesn’t allow enough sunlight for seagrass to survive. Without seagrass beds, algae cells proliferate and die off quickly. As a result, their decomposition adds nutrients to the water and phosphorus accumulates.

“This conversion from a bay that was dominated by seagrass on the bottom to a bay that now is prone to these big algae blooms that are up in the water column, that’s where the tipping point is,” Crowl said.

While there have been efforts to restore seagrass beds and some have started to regenerate, the bay’s seafloor is still largely barren. Crowl said FIU is working with a community to 3D print blocks of “eco-crete,” a type of carbon-absorbing concrete, to plant seagrass beds.

An algae bloom photographed in Coral Gables, Miami, in August 2020. Image courtesy of Danoushka Capponni / Miami Waterkeeper.

FIU is also working on a chemical fingerprinting method of tracing phosphorus molecules to their source in an effort to prioritize communities causing the greatest amounts of phosphorus pollution, usually from old septic tanks.

“The intent there is to basically give the city a blueprint for where they can get the biggest bang for their buck in terms of taking out septic systems and replacing them with sewer systems,” Crowl said, adding that areas with the oldest septic system infrastructure are often inland and located in low-income areas where people can’t afford to pay for septic tank replacements.

Since the August 2020 fish kill, Crowl and directors of other environmental resource agencies have convened for monthly meetings to discuss their data and strategize how to move forward on solutions — quickly.

“There’s a new political will,” Crowl said. “This last fish kill pulled the community together.”

The FIU Institute of Environment team set out on Biscayne Bay during the August 2020 fish kill to assess the situation and deploy its CREST buoys to collect water quality data. Image courtesy of FIU Institute of Environment.

From reactive to proactive: A bay health wellness check

When pufferfish and barracudas turned up dead on the bay’s surface waters, citizens and research teams flocked to the bay to remove dead fish and collect data.

Among them was FIU’s Institute of Environment team. The CREST Center for Aquatic Chemistry and Environment deployed a research buoy that detected the bay’s high water temperatures and low dissolved oxygen levels, providing scientists with clues to the cause of the fish kill.

Gregory Murad Reis, an assistant professor at the Knight Foundation School of Computing and Information Sciences and researcher at FIU’s Institute of Environment, is part of a team using automated vessels, or remote-controlled robots, to collect data and learn more about Biscayne Bay’s habitats and hydrology.

An underwater vessel resembling a torpedo collects data on oceanic conditions at 1-second intervals as it moves through the water, including dissolved oxygen levels, temperature, salinity, blue-green algae and other parameters to measure water quality. It can also dive down to 200 meters (660 feet) deep, Reis said, and can be controlled manually or programmed to navigate the waters on its own.

Their surface vessel, on the other hand, uses remote sensing to help scientists construct maps of the seafloor, better understand water currents, take images of wildlife and collect water samples for lab analysis.

By collecting the data in different areas of the bay over time, Reis said they hope the robots can help increase preparedness for when the bay passes another tipping point.

Elizabeth Kelly, Miami Waterkeeper Water Quality Research Manager, collects environmental data during water sample collection at Morningside Park during the August 2020 fish kill. Image courtesy of Miami Waterkeeper.

“We can build predictive models in the future, and they can serve as an early alarm system in case something as tragic as a fish kill might be prevented,” Reis said. “We were really good at reacting to these events, but now we should be able to predict when they might occur.”

Tipping points aren’t necessarily a death sentence for ecosystems like Biscayne Bay, notes Kevin Boswell, a marine ecologist and associate professor at FIU’s Institute of Environment.

“Systems that undergo huge stresses that could possibly be beyond tipping points can be fixed,” Boswell said. “If the effort is put forth to rectify the problems and identify where the biggest sources of harm exist … it can be reversed.”

Biscayne Bay supports a variety of species, from its iconic megafauna — such as rays, dolphins, manatees, lobsters, wading birds and popular game fish — to invertebrates and microbes. This biodiversity is largely dependent on healthy coral reefs, seagrass beds and mangroves forests.

“It’s not too late, but these habitats are critical for preserving the connectivity and the diversity of this system,” Boswell said.

Some species migrate through different parts of the system, he explained, and while it’s biodiverse, there are also invasive species that cause additional problems. Notably, lionfish have wreaked havoc on the reef ecosystems, and a coral disease has now spread as far south as Dry Tortugas National Park, south of Key West in the Caribbean.

“With a suite of these [robots] operating all at the same time in different areas, we can get information simultaneously across broad scales that helps [us] really understand the patterns and connectivity of an ecosystem, and in addition, how organisms may be using it or moving through it,” Boswell said.

While FIU’s automated and remote-controlled vessels offer an opportunity to learn more about how the ecosystem functions and can help detect when it’s off-balance, Boswell stresses the importance of minimizing further harm to the environment.

“If you continue to impact the coastal zone, you’re going to ultimately pay the price for what you’ve done. It’s a natural barrier,” Boswell said, explaining that natural coastlines with structures like mangroves mitigate the effects of sea level rise and storms. “If you remove those, then their natural function is removed as well.”

A dead fish lies beneath a cluster of oyster shells at Pelican Harbor Boat Ramp in Miami, Florida, during the August 2020 fish kill. Image courtesy of Josephine Caffin.

Citizen science looks to oysters as a natural remedy

Miami business owner Alberto Aran, who goes by Tico, grew up in Miami a dedicated boy scout, spending his days camping, diving and spearfishing in Biscayne Bay with his dad. Now a father himself and an advocate for the bay, he’s pioneering a project using oysters as a nature-based solution to help prevent tragedies like the die-off.

In the weeks following the fish kill, and as the pandemic continued to keep Floridians bound to their living rooms, Aran took one of his daughters out for some fresh air on an impromptu field trip to search for oysters. They started finding them in small pockets along the coastline, he said.

Aran had heard about the ability of oysters to filter pollutants: they eat algae, and a single oyster can filter up to 190 liters (50 gallons) of water a day in addition to other ecosystem services. To his surprise, using oysters to remediate the bay wasn’t a big topic of discussion at community meetings and among scientists.

It turns out it has a lot to do with the lack of freshwater flow into the bay.

“I didn’t know how water flowed in my own backyard,” Aran told Mongabay in an interview. “What was the water flow back then, what is it today, and where are the places in the bay where we can put some natural implements in place to help…restore the habitat?”

Today, it’s rare to find native oysters in the bay compared with historically. Eastern oysters (Crassostrea virginica) were once populous, according to an 1896 commissioner’s report on Biscayne Bay for the United States Commission of Fish and Fisheries, and are considered a keystone species. Oyster beds reportedly attracted fish like red drum (Sciaenops ocellatus) and black drum (Pogonias cromis), which aren’t common in the bay anymore, either, although Aran says he’s personally seen black drum recently near existing oyster beds. The northern part of the bay even supported an oyster fishery until the 1920s.

Alberto Aran holds an aquaculture cage he found washed up on Elliot Key in Biscayne National Park. Aran began his citizen science-driven project to help re-establish oyster beds in Miami waterways in December 2020. [Right] Oysters cling to the mangrove roots at Oleta River State Park on Biscayne Bay in North Miami. Images courtesy of (left) Alberto Aran and (right) Marlowe Starling.

Researchers largely attribute the oysters’ decline to South Florida’s water diversion projects, restricting what was once a continuous flow of freshwater. Eastern oysters thrive in brackish water, which is a mix of fresh and salt water, and require a low salinity level to survive. However, other oysters, such as the flat tree oyster (Isognomon alatus), can tolerate higher salinity levels.

As Aran continued researching on his own, he found that the only places habitable for native oysters were canals and other waterways — some of the only places where the water is consistently brackish year-round.

At first, Aran kept just 10 to 15 oysters alive in a simple dive bag behind his parents’ house, and after about eight months, the colony grew to an estimated 40,000 oysters. Aran said he has recently spotted species he and other locals have never seen there before, like red drum, indicating increased biodiversity.

By December, Aran had officially launched his project to reestablish oysters in the bay at two main sites using the help of the community, such as a campaign to collect oyster shells from local restaurants. In late June, when Aran spoke with Mongabay, he said they had collected close to 50,000 shells and raised $15,000 through the project’s fundraising page — more than double the original goal.

“This is really a citizen science push to get this started,” Aran said.

Before they can be used, the collected shells have to be cured for three months, meaning they sit outside in the sun and rain to kill any nonnative life that may be attached to them. The shells are then ready to be hung on lines or placed in cages under people’s docks to serve as a landing site for free-floating baby oysters that can die if they land in the mud. The cages help protect the oysters from predators, such as spotted eagle rays (Aetobatus narinari), sheepshead (Archosargus probatocephalus), red drum and otters.

“If we give [oysters] assistance, they’ll thrive where they can find the habitat,” Aran said. “They will find those locations as things improve and as we increase the amount of freshwater that’s flowing through Biscayne Bay.”

Aran said he also plans to start a citizen science monitoring program to encourage residents to record data on oyster presence by walking or kayaking along canals and mangroves where the oysters colonize. He said he’s never seen support for Biscayne Bay conservation at the level it’s at now, making him hopeful the project will continue to grow.

Aran added that losing seagrass means losing ecosystem balance, carbon sequestration, storm protection and a nursery for fish, such as economically important pink shrimp (Farfantepenaeus duorarum) and stone crabs (Menippe mercenaria), two examples of Florida marine species that people depend on as a source of income.

“Our ecosystem, it’s teetering on the edge. We need to clear up the water table so the seagrass can return,” Aran said. “We should be teaming up with nature and trying to find out where she can help us.”

Eastern oysters are filter-feeders for algae, which means they help extract nutrients and create clean water. [Right] Volunteers string oyster shells on a line. Images courtesy of Alberto Aran.

Biscayne Bay gets a voice

In the months following August’s fish kill, efforts to conserve and restore the bay did seem to amplify. Environmental activists and scientists continued to call for legislative action after months of suggesting the same solutions to old problems had not been implemented.

A recovery plan for the bay was approved by county commissioners by October, a detailed management report led by Irela Bagué, who at the time chaired Miami-Dade county’s Biscayne Bay Task Force, a group of people who analyzed data, made recommendations for legislative action and produced a report detailing areas of improvement.

In January 2021, Bagué made history. She became Miami-Dade’s first chief bay officer: a new position dedicated to advising county officials on matters and projects relating to the health and restoration of Biscayne Bay, such as a recent fertilizer ordinance to reduce nutrient pollution during the rainy season.

“We look at Biscayne Bay as our Central Park,” she told Mongabay in an interview. “There’s a lot to lose here.”

Her motto: “The environment is the economy.” Bagué likes to say that the South Florida economy depends on a healthy Biscayne Bay.

“When seagrass goes, so does fishing, so does everything else,” she said. “It’s the lifeblood of our underwater wildlife, so there’s a lot at stake.”

In 2019, Biscayne National Park alone attracted 709,000 visitors who spent $46 million in nearby communities, according to the National Park Service. All South Florida national parks combined, including the Everglades, Dry Tortugas, Biscayne and Big Cypress, contributed more than $352 million to the South Florida economy.

A brown pelican (Pelecanus occidentalis) swoops over Biscayne Bay at the Deering Estate. Image courtesy of Elias Horna.
A mangrove cuckoo (Coccyzus minor) rests on a branch. Image courtesy of Elias Horna.

Multimillion-dollar bayfront condos and Miami’s reputation as a cruise capital speak to the importance of a clean and healthy bay, Bagué said — one that isn’t brown with seaweed, dead seagrass and algal blooms.

Even beyond its aesthetics, residents depend on a functioning ecosystem for survival. Sea level rise caused by climate change threatens to contaminate underground aquifers with saltwater in a process called saltwater intrusion. Florida’s aquifers, including the Biscayne aquifer, supply 90% of the state’s drinking water.

With the fish kill’s one-year anniversary right around the corner, communities along Biscayne Bay are left wondering if the shoreline will be littered with dead marine life again this year. If it does happen, Bagué said the county is working on a fish kill response plan to be better prepared, which includes partnering with compost company Fertile Earth to dispose of dead biomass.

“Let’s stop the bleeding and then treat the disease,” she said.

As politicians, citizens, scientists, activists and others in the community seek answers for the bay they depend on, plenty of questions remain about the future of Biscayne Bay. But with increased cooperation among different groups of people in the South Florida community, there may be hope for its future.

“Everybody is talking,” Aran said, “for the first time in a long time.”


Parker, M. L., Arnold, W. S., Geiger, S. P., Gorman, P., & Leone, E. H. (2013). Impacts of freshwater management activities on eastern oyster (Crassostrea virginica) density and recruitment: Recovery and long-term stability in seven Florida estuaries. Journal of Shellfish Research, 32(3), 695-708. doi:10.2983/035.032.0311

Robblee, M. B., Barber, T. R., Carlson Jr., P. R., Durako, M. J., Fourqurean, J. W., Muehlstein, L. K., … Zieman, J. C. (1991). Mass mortality of the tropical seagrass Thalassia testudinum in Florida Bay (USA). Marine Ecology Progress Series, 71, 297-299. doi:10.3354/meps071297

Lirman, D., Thyberg, T., Santos, R., Schopmeyer, S., Drury, C., Collado-Vides, L., … Serafy, J. (2014). SAV communities of western Biscayne Bay, Miami, Florida, USA: Human and natural drivers of seagrass and macroalgae abundance and distribution along a continuous shoreline. Estuaries and Coasts, 37(5), 1243-1255. doi:10.1007/s12237-014-9769-6

Millette, N.C., Kelble, C., Linhoss, A., Ashby, S., & Visser, L. (2019). Using spatial variability in the rate of change of chlorophyll a to improve water quality management in a subtropical oligotrophic estuary. Estuaries and Coasts, 42(7), 1792-1803. doi:10.1007/s12237-019-00610-5

Banner image: A dead pufferfish at Morningside Park in Miami, Florida, during the August 2020 fish kill. Image by John Cline.

Exit mobile version