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Restoring Habitat, Fostering Fisheries

Looking back across more than a decade of habitat restoration work, Bonefish & Tarpon Trust scientists and partnering agencies check in on five projects in five counties, all part of a big-picture approach to helping Florida’s fisheries thrive.

BY ALEXANDRA MARVAR

Have you seen Bonefish & Tarpon Trust’s name pop up in the context of wildlife refuges, land development projects and more across the state of Florida? That’s because the organization has been focused, for more than a decade, on habitat restoration as a strategy for preserving and fostering one of the state’s most valuable assets: its sport fisheries. And over and over again, studies show that when it comes to preserving fisheries—and keeping anglers fishing—habitat is where it’s at.

Scientists have found that when land in coastal areas or in wetlands, marshes, or river systems is lost to or changed by things like residential or commercial development, the fish that depend on these habitats are affected. Water quality degradation, heavy boat traffic, dredging or other changes to the way water moves through the area also mean the fish and their prey will be less able to travel, live or spawn there the way they did in the past. A Florida Fish and Wildlife Conservation Commission study of all Florida’s vertebrates found that 44 percent of these species are known or suspected to be declining in number or distribution. Meanwhile, close to a quarter of the approximately 1,200 species tracked by the Florida Natural Areas Inventory are expected to lose at least 50 percent of their range to sea level rise in the coming 75 years. Habitat loss to human development, scientists say, is an even greater—and more immediate—threat.

All of this is further exacerbated by climate change. And according to BTT Juvenile Tarpon Habitat Program Manager JoEllen Wilson, where habitat is degraded or ruined, fish populations will never be as productive as they were historically, no matter whether there are anglers around to catch them or not.

Rookery Bay, Florida. Photo: Rookery Bay National Estuarine Research Reserve

Wilson has been researching juvenile tarpon habitats for well over a decade, learning from natural habitats, designing for and then monitoring restored ones to understand what’s working and why. Right now, she’s focused on Charlotte County—home to Boca Grande, known by many as the tarpon fishing capital of the world—and it’s a place she knows well: She was born here, and she grew up fishing here. It gives her a good baseline, she says, for what she wants to achieve with her habitat restoration work— for what’s possible.

“When people move here and talk about the fishery, it’s like ‘Man, you should have seen it when I was 12 years old,” she says. “Someone that came later in life, not knowing how good it was, just may not see it the same way that I do.”

Studies indicate that as of now, Florida has lost about 50 percent of the mangrove habitat it once had. “We’re past the point of just being able to protect what’s left,” Wilson said. “We’ve got to start restoring anything that we can.”

BTT has long been dedicated to providing scientific research to inform and guide conversations about fisheries management and habitat changes. But the stewards of Florida’s fisheries aren’t stopping at data collection: They’re getting their hands dirty. Together with a number of partners from government agencies to non-profits, BTT works to identify optimal habitats that are at risk of damage or disappearance, or that are already being degraded, and intervene to save and restore them.

JoEllen Wilson samples baby snook and tarpon at the Coral Creek restoration site in Southwest Florida. Photo: FWC

What’s this mean exactly? It means, Wilson says, that Florida’s most heavily developed and altered marine and aquatic ecosystems are going to need to undergo some drastic changes.

“Our intention is for everybody to be able to fish forever—to conserve fisheries for everyone’s enjoyment,” she says. “If we can make some big changes now, those will have a really heavy and sustainable impact.”

BTT has partnered on restoration projects in The Bahamas and across the state of Florida. Now, JoEllen’s team is working directly with the Florida Fish and Wildlife Conservation Commission (FWC), researchers at the University of Florida, and other partners to design a new way to manage fisheries that includes habitat: both protecting natural habitats that are not yet degraded or destroyed, and restoring habitats that are still within reach of saving.

A SHIFTING BASELINE

BRADENTON, MANATEE COUNTY | ROBINSON PRESERVE EXTENSION

BTT partner Damon Moore, founder of Oyster River Ecology habitat restoration consulting practice, draws motivation for his work in Manatee County from a similar source. At the southern edge of Tampa Bay, Moore has been working on a 600-plus acre project called Robinson Preserve. The newer Robinson Preserve Expansion phase was designed to create habitats for juvenile fish by building on earlier restoration work and incorporating research findings and data-driven design input from partners including BTT. When he imagines what’s possible for this site, he thinks about what it was before humans intervened.

An excavator making final grade adjustments just after the created basin was connected to tidal waters. Photo: Damon Moore

“We’re definitely victims of a shifting baseline,” Moore says of Florida. “People constantly move here, and they see that it’s beautiful. There are fish in the water. But they have no concept of what it was like 50 or 100 years ago. We don’t have this generational understanding of what this land looks like. There’s a constantly shifting sense of place.”

And he’s already seen, over the course of his nearly 20 years working in this field and 10 years at Manatee County, some tremendous evolution: Not only does the preserve host tarpon and snook—it’s also a haven for migratory birds, gopher tortoises, even the occasional dolphin or manatee.

“Never in those early discussions did we say, ‘We’re going to create manatee habitat.’ But now they’re coming up there. Everybody loves a manatee. And when you think of it in the context of how this used to be really beat-up former agricultural land, and now there’s manatees making use of it, and finding refuge and food in these places, that’s a pretty awesome thing,” he says.

Created oyster reefs exposed during a winter low tide. The project included 2.1 acres of oysters which filter water and provide habitat for multiple organisms, including prey species that feed juvenile snook and tarpon.
Photo: Damon Moore

At nearby Perrigo Preserve—another former agricultural site in a coastal setting that was restored—Moore was able to help create the conditions to reintroduce federally endangered plant species. There have been some big victories, he says, but there’s a great deal of work left to do here in Manatee County, and no time to delay. Habitat restoration decisions need to be backed by science and informed by data, he said. He also wants to see these projects happen fast.

Big ideas call for big teamwork. Organizations like the Manatee County Audubon Society and the Girl Scouts of the Gulf Coast are leveraging Moore’s expertise in oyster habitat restoration and ecological restoration planning and management at their own sites while changemakers like Parks and Natural Resources Department’s Charlie Hunsicker—who helped shape the original plans for Robinson—are helping to move large-scale projects forward at the county level. This past December, the county submitted a bipartisan infrastructure bill grant for $14.7 million to undertake ecological restoration projects, including a lot of oyster work up and down the Manatee River.

“Given the urgency of need [...] we need to learn as we go. We’re behind the curve as far as what we need to restore, but at the same time, you can’t do anything without having that research behind it to know what you’re doing—because you could waste a lot of money if you don’t,” Moore says. Being equipped with early input from BTT on the work at Robinson could help speed up the process in future project design.

RESTORING HABITAT VS. RESTORING HYDROLOGY

NAPLES, COLLIER COUNTY | ROOKERY BAY NATIONAL ESTUARINE RESEARCH RESERVE

The work at Robinson Preserve is a great example of habitat restoration at work, where earth was moved to reshape the land into very specific topographical and water features, and paired with management strategies to make way for native flora and fauna. Hydrologic restoration is part of the habitat puzzle, too. Essentially, Wilson explains, hydrological restoration involves “poking holes in places where there should be holes but aren’t any longer because of human actions” with the aim of recreating a site’s natural watershed flow.

Culverts implemented during road construction aren’t always conducive to fish passage. The preliminary design plan for Marco Shores Lakes is to adjust or replace this culvert to allow juvenile sportfish passage from the connected tidal creek in and out of Marco Shores Lake. Photo: JoEllen Wilson

For example, in Collier County, just 60 miles from tarpon hotspots Boca Grande and Sanibel at Rookery Bay’s Fruit Farm Creek, restorers are applying hydrologic interventions to reconnect hundreds of acres of mangrove habitat and marshland with water, flowing the way it had before human intervention.

Decades ago, road construction here—between Marco Island and neighboring Goodland—cut off the upper tidal creek reaches from the coastal waters, disrupting natural water flow patterns and leading to the loss of 60 acres of mangrove trees.

Scientists found that disruption wasn’t just killing off mangroves—it was directly affecting sportfish populations. In high-tide events, when the roadways would be breached by flooding, tarpon and snook were crossing from one body of water into the other, becoming trapped. The water flow between these bodies of water “needs to reconnect at least seasonally, if not monthly or at normal high tides,” Wilson says, to allow for tarpon and snook movement.

Sportfish depend on calm backwater areas and embayments once they emigrate from the nursery habitats. Photo: JoEllen Wilson

In the wake of Hurricane Irma, BTT and project partner the Florida Department of Environmental Protection (FDEP), led the grant funding, provided by the National Fish and Wildlife Foundation (NFWF) and the State of Florida, for two hydrological restoration projects here to set this waterflow right again. Habitat assessment and preliminary design took two years to complete and BTT received funding for final design and permitting to be completed in 2025. According to the FWC, it’s considered the largest mangrove restoration of its kind in state history.

BTT’s habitat restoration projects benefit juvenile tarpon, snook, and their prey. Photo: Aaron Adams

The plan leveraged culvert pipes and removing sediment to restore tidal flows, improving water-carrying capacity and wildlife access. After restoration, tidewaters will reach 209 acres of previously impounded wetland, relieving stressful conditions for remaining mangrove trees, promoting seedling growth, and averting disaster.

“By punching holes in those roads, or creating wildlife crossings in the form of bridges, or larger culverts, or just waterway passages, you’re reconnecting that habitat,” Wilson says. “You’re also creating more habitat, by [creating] access to more habitat that wasn’t initially there.”

INNOVATIVE NEW APPROACHES

GIBSONTON, HILLSBOROUGH COUNTY | KRACKER AVENUE

Now, let’s combine them: Some projects require both habitat restoration (earth-moving) and hydrological restoration (water flow). This is complicated stuff, and Bart Weiss, Chief Officer of Innovation and Resiliency at Hillsborough County and as of December, President of the National Water Reuse Association, said it takes some forward-thinking plans and some innovative strategies.

Weiss’s office has spearheaded some massive water reuse initiatives that involve pumping billions of gallons of highly treated, potable reuse wastewater (clean enough to drink, or make beer from, Weiss’s office has shown) into the water table to offset freshwater usage near the coast, pressurize the aquifer, and prevent cataclysmic saltwater intrusion. But he’s also helped guide a takeover and reimagining of a series of former tropical fish farming ponds on Kracker Avenue. At this site, Weiss’s office and partners including the Southwest Florida Water Management District (SWFWMD) and BTT worked together to redesign this landscape for the better. Construction is next.

“As people have built along the shorelines around Tampa Bay, we’ve lost fish habitat, juvenile fish habitat, estuarine-type habitat,” Weiss says. “We bought this piece of property and it has 235 fish tanks. Then we started thinking about taking reclaimed water, creating a different pond system here, and dropping reclaimed water into it.” The plan, he explained, will yield a tidal lagoon, complete with mangrove islands, that has a connection to nearby Schultz Preserve, as well as flow to Tampa Bay.

“This will be tidally controlled, it’ll be brackish water, so now you’ll have consistent flow of freshwater down into a tidally affected area, and then flow continues out so it’ll be a fresher water flowing out,” Weiss says, “so there’ll be a signature there for juvenile fish to pick up and come in.”

PROJECTS THAT CAN BE TEMPLATES FOR FUTURE RESTORATION WORK

CAPE HAZE, CHARLOTTE COUNTY | CORAL CREEK

These hydrologic and habitat restoration efforts can have big local impact when it comes to expanding the viable territory for native and endangered Florida flora and fauna. But they’re also significant regionally—and they might have even broader benefits.

Robert McDonald, an engineer with SWFWMD, is overseeing the design and construction of the Cape Haze Restoration Project. It’s taking place at Coral Creek, the site of an abandoned residential project within the Charlotte Harbor Preserve State Park near the Boca Grande Pass. Now, it’s co-owned by SWFWMD and FDEP, and SWFWMD-led projects are underway to restore both habitat and hydrology of this site containing “a mosaic of critical coastal habitats.”

The canals at Coral Creek during restoration. Photo: SWFWMD

Before public ownership, McDonald says, construction, ditching and dredge-fill on the site changed the hydrology. Today, six adjacent canals are connected by a main canal that has an inlet to the creek’s west branch. SWFWMD had initially considered filling in these six canals, returning them to their natural pine flatwood topography. But after discovering the presence of juvenile tarpon, they pivoted. As Wilson points out, these canals are actually the perfect location to test various tarpon nursery habitat designs, yielding data that can help outline restoration projects at similar sites in Charlotte County, across Florida, and even other places in the coastal U.S. grappling with similar ecological challenges.

One of the canals at Coral Creek after restoration. Photo: FWC

BTT scientists looked at previous research to outline the ideal habitat characteristics for juvenile tarpon and then in collaboration with scientists at the Charlotte Harbor National Estuary Program and FWC, they created three experimental designs to be duplicated and tested across the six canals in order to determine how those different characteristics drive change.

They focused on juvenile tarpon, and that doesn’t mean they’re ignoring other species, Wilson notes: “Working with SWFWMD on this project, we wanted to show that you can focus on a singular habitat, and do it really well—and you’re really protecting a high number of species and creating a higher-quality habitat.”

The restoration treatments being tested at Coral Creek.

BTT and FWC conducted monthly sampling at Coral Creek, including tagging all captured juvenile tarpon with passive integrated transponder (PIT) tags, detectable by antennae that act like a toll booth clocking tarpon as they pass through the canals. Once the team knows what tarpon prefer, Wilson says, they can replicate the favored design elements in future habitat restoration projects.

Planning is underway for the next Phase at Coral Creek—and then there will be earth-moving. The next phase, McDonald says, will be to restore on-site hydrology which had been adversely impacted by past construction activities.

BTT is coordinating with FWC to monitor the progress. Just looking at “before” and “after” data for early phases of the Coral Creek project, Wilson says, the tarpon population already appears to be experiencing benefits. The individual rate of growth doubled after the initial phases of habitat restoration.

“With every project there are lessons learned that we apply to the next project and work smarter,” McDonald says. Partners hope the learnings have positive impacts far beyond these six canals.

DESIGNING FOR A DEEPER UNDERSTANDING

VENICE, SARASOTA COUNTY | ALLIGATOR CREEK

Speaking of broader impacts, Alligator Creek in Sarasota County is a long-term habitat restoration project that can tell us a lot about the future of human habitation and healthy fisheries, Wilson says.

In the 1940s, this 11-square-mile tidal creek in Venice was excavated, channeled, and cut off from the floodplain and nearby wetlands. Today it’s a draining channel into Lemon Bay, lined with eroding banks and invasive vegetation. But still, it’s an ecosystem for marine life, birds, and endangered animals. Degrading conditions threaten the balance here, and a large-scale, longterm, multi-pronged habitat and hydrologic restoration project is just in the planning stages now, led by Sarasota County Public Works.

Mote Marine Laboratory and Aquarium is doing the monitoring on the project, and BTT has provided juvenile tarpon and snook input, which involves cleaning up an entire creek system—one that will continue to flow through a developed location. Is it even possible? “This is going to have really big impacts,” Wilson says of the project. It should help Florida answer questions like: “Can we feasibly all live together in harmony? Can we have viable nursery habitat for multiple species and human development adjacent to that?”

CONSERVATION AT A CROSSROADS

These sites aren’t the only things that are changing—the way these projects are approached and implemented is evolving on a fundamental level: Trans-disciplinary collaboration is becoming more common. The necessity of consistent monitoring, including before work breaks ground, is being emphasized. And decisions about what sites to restore and how to treat them are becoming more data-driven, Wilson says.

“We’re at the crossroads right now,” she adds. “Up until this point, every agency has been kind of doing their own ‘restoration.’ But by doing these very targeted restoration efforts, and then publishing our data, we’re showing you can have well-monitored, detailed, targeted designs, and you can show success, not just in terms of ‘before’ and ‘after,’ but success in relation specifically to your designs.”

SMALL SITES, BIG CHANGE

Some of these projects are sprawling in size and scope—some are relatively bite-size. But they’re all part of a much bigger picture, of a better, biodiverse future. With no fewer than 12 projects behind them, there’s no slowing down now, Wilson says.

“I’ve got six more potential projects on the docket in the site selection phase. We put in for funding to do a habitat assessment and a preliminary design to look at feasibility, so we’re waiting to see if we get grant funding to move that through the pipeline.” And there are many, many more sites to choose from beyond these six: “I’ve got over 300 identified juvenile tarpon habitat locations throughout Florida, so although we’re focusing in Charlotte County, we’d really like to see this replicated in other areas,” she says.

“Right now, our biggest issue for fishing in Florida is not overfishing—it’s declining habitat, and that’s why we’re trying to approach fisheries conservation from different angles,” she adds. “So, in addition to our focus on habitat protection and restoration, we’re also addressing water quality through our studies of pharmaceutical contamination and wastewater treatment upgrades. If we can do this right, the fish will be there. They’re resilient—to a point.”

Alexandra Marvar is a freelance journalist based in Savannah, Georgia. Her writing can be found in The New York Times, National Geographic, Smithsonian Magazine and elsewhere.

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