NOAA Is Restoring A Pristine Estuary — With Help From A Lot Of Friends

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When I first relocated to southeast Florida, neighbors invited me to watch the buoyant manatees lounge and dive in the marina area. Oysters clung to the Indian River’s shorelines and dock areas. Fish jumped around us as we kayaked through the mangrove channels. At sunset, we’d bike down the road and look for dolphins with the last light.

That ecosystem magic changed between 2011 and 2020, when widespread harmful algae blooms killed an estimated 89% of the estuary’s seagrass. Between December 1, 2020 and April 30, 2022, the unprecedented number of 1,255 manatee carcasses was documented and 137 rescues were conducted along our coast — manatees cannot survive without seagrass. “We’re still in the very early stages of recovery,” says Duane De Freese, executive director of the Indian River Lagoon Council. “We lost more than 140,000 acres of seagrass, and we’re not going to outplant our way out of that.”

What will it take to restore a 156-mile-long estuary? How can policy reinvigorate what were once expansive seagrass beds, abundant fish and wildlife, and clear water? Pollution, habitat loss, and harmful algal blooms — and the sources of these habitat destroyers — need to be addressed. The Indian River Lagoon (IRL)  Council has been given an enormous task — to embark on an ecosystem-wide effort to revive one of the world’s most pristine estuaries. A huge team of five federal agencies, two state agencies, three local government entities, four academic institutions, six nonprofits, sixteen consultants, and a 2,400-member volunteer force have been entrusted with the project.

Sounds like a red tape nightmare, doesn’t it?

It will take every nickel of the $9.4 million allotted from NOAA Fisheries’ Office of Habitat Conservation to rejuvenate the IRL, which is part of the US National Estuary Program. It is considered an estuary of national significance and one of the most biologically diverse estuaries in the US. More than 4,300 species are dependent upon its ecosystem for some period of its lifecycle, and fifty of these species are endangered or threatened.

The Indian River is misnamed, as it is not a river: it is an estuary and a lagoon. Cooler waters from the north mix with warmer waters from the south, so that the lagoon’s geography is a biodiversity oasis with more than 4,000 species of plants and animals from temperate, subtropical, and tropical zones. The IRL is a network of ecosystems: seagrass meadows, mangrove forests, salt marshes, oyster reefs, and tidal flats.

Saltwater and freshwater merge meet to form brackish water, which acts as a protective barrier for young fish, crabs, and shrimp as they mature. The site’s mangrove wetlands and salt marshes provide breeding, nursery, and feeding areas for a variety of organisms. These coastal areas also filter runoff, stabilize sediments, maintain water quality, and protect shorelines from erosion.

Its narrow and shallow dimensions, with only five restricted ocean access points, however, means that the IRL estuary is less affected by tides than other estuaries. So, “what goes in the lagoon from the land often stays in the lagoon,” explains De Freese.

Killing It Softly with Damaging Nutrients

The IRL is within an easy drive of 3.5 million people in seven counties and 38 cities and towns. This outer area is the source of damaging nutrients from agriculture, stormwater runoff, wastewater, and septic systems. Estuary ecosystem functions have been severely diminished due to decades of urban and agricultural misuse that have altered natural hydrologic processes.

“The Indian River Lagoon is super complex to manage and restore because it’s not just one system,” said De Freese. “It’s multiple systems, each with different stressors, so you have to approach restoration in a way that recognizes that complexity. That’s why we asked NOAA to fund a mosaic of habitat restoration projects.”

The goal is to restore four critical habitat types: coquina rock reefs, shellfish beds, seagrass meadows, and wetlands.

Reefs: Spartan Reefs are compact, cross-shaped concrete structures reinforced with fiberglass rebar to prevent corrosion. Each unit weighs about 50 pounds and can be carried and installed by hand, often beneath docks near seagrass beds or shorelines. Barnacles, mussels, and other filter-feeding species are already encrusting the structures, attracting shrimp, crabs, and other predators.

Shellfish: Oysters filter four gallons of estuary water each hour and have been a food source for area people for centuries, as confirmed by shell middens at local archaeological sites. Beyond serving as food for people and marine animals, clams also make food for other species as they filter out algae and food particles. Shrimp, crabs, and fish gobble up these highly nutritious snacks. Yet clams became virtually extinct in the IRL. Overharvesting, large freshwater discharges from Lake Okeechobee, and stormwater runoff from urban areas caused a series of massive algal blooms in “a kind of environmental apocalypse,” states University of Florida professor Todd Osborne, who is leading clam restoration efforts for the estuary.

Seagrass: Seagrass meadows once served as the foundation of the Indian River Lagoon’s food web. Manatees and other herbivores graze on seagrass, while the plants shelter juvenile baitfish such as pinfish, mullet, and mud minnows. Those fish, in turn, support larger species including red drum, spotted seatrout, tarpon, and flounder. Seagrass also improves water quality by stabilizing sediment and preventing it from clouding the water. In the IRL, a combination of improperly treated sewage, leaking septic systems, fertilizers, and stormwater runoff has led to eutrophication. This means that frequent harmful algal blooms have blocked the light necessary for photosynthesis.

Wetlands: Wetlands maintain the health of the IRL and protect the adjacent coastal communities. They filter out pollutants that reduce water quality and trigger harmful algal blooms. Wetlands are also habitat for fish, birds, and other wildlife. Studies estimate that healthy wetlands can produce about 50 pounds of live fish per acre annually. In addition, wetlands protect communities from flooding by reducing wave and storm surge impacts. Large areas of IRL coastal wetlands were converted into mosquito control impoundments with miles of dike separating the wetlands from the lagoon. These barriers disrupted natural water flow and limited the movement of fish and other species.

How do You Solve a Problem like Estuary Pollution?

In total, the IRL project is in the process of restoring the following elements of the complex estuary system:

• Outplanting 21 million clams.
• Restoring 8,450 linear feet of shoreline.
• Outplanting 6,985 units of salt marsh grass.
• Reconnecting 2,125 acres of wetlands.
• Outplanting 2,300 mangroves.
• Restoring 45 acres of seagrass.
• Restoring 7 acres of oyster reefs.
• Pilot testing three small artificial coral reefs.

Some practitioners now describe a cautious but positive shift in momentum. They point to seagrass beginning to reappear in places where it had vanished and to degraded wetlands blossoming with greenery months after being reconnected. Outplanted clams are still growing two years after being placed in the wild, another positive sign.

NOAA funding helped the Council to assemble a broad partnership of restoration practitioners to tackle the complex problems facing the lagoon. They are sharing information and joining together to tackle shared challenges.  While some of these projects are already complete, several will take another year or so to finish. More funding will provide project assessment through ecosystem response. As time evolves, the Council and its partners will developing additional, separately-funded restoration projects, like Brevard County’s offer to homeowners of up to $20,000 to upgrade septic systems to reduce sewage entering the lagoon.

Show Me the Money from the Estuary

While many of us reading this article may solely savor the IRL estuary due to its vibrant marine ecosystem, much is made of its contributions to the local economy — reported to comprise one-seventh of the region’s total economy. The Balmoral Group calculated in 2025 that the lagoon generates $28.3 billion in local economic activity each year.

Importantly, on average, every dollar invested in restoration yields about $24 in public benefits.

“People tend to think of restoration as a cost alone rather than considering long-term benefits and value,” Freese reminds us. “But when you look at what these habitats provide, it pays dividends.”

Resources

• “A system-wide effort to restore Florida’s Indian River Lagoon.” NOAA. February 26, 2026.
• “Closed manatee mortality event along the East Coast.” Florida Fish and Wildlife Conservation Commission. 2026.
• “Ecology of the Indian River Lagoon.” Florida State Parks. 2026.
• “Investing in Indian River Lagoon restoration pays dividends.” NOAA. February 27, 2026.
• “Indian River Lagoon Economic Valuation.” Balmoral Group. October 2025.
• “Restoring the Indian River Lagoon’s seagrass meadows and wetlands.” NOAA. March 05, 2026.
• “Restoration innovation on the Indian River Lagoon: Spartan reefs, super clams, and more.” NOAA. March 04, 2026.
• “Trouble for manatees in the Indian River Lagoon.” Save the Manatee. 2026.