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Seagrass 101: Understanding the Problem

Getting to the roots of a tough, troubled plant

Seagrass 101: Understanding the Problem

Many ocean species, including this mutton snapper, depend on healthy grassflats at key points in their life cycles. 

Dennis Hanisak’s head emerges from the Banana River, water beading on his snorkel mask. “Something is grazing in here,” he says. “They’re much shorter than they were.”

It’s September, and we’re wading between rows of farmed seagrass nestled against Samsons Island, part of an experimental restoration project led by the City of Satellite Beach in collaboration with the National Estuary Program.

Hanisak, a research professor at Florida Atlantic University’s Harbor Branch Oceanographic Institute (HBOI), has studied seagrass since the early 1990s. He’s here to monitor the progress of 350 planting units of nursery-grown shoal grass, Halodule wrightii, secured to the bottom of the Indian River Lagoon with shish kabob skewers. The west side of Samsons Island used to harbor about 35 acres of seagrass, but has been bare for the past eight years. This project is one of many in the lagoon, all begun with the aim of finding the best means of replacing seagrass in an ecosystem where about 75% of acreage has vanished since 2009, with some areas experiencing a near-total loss.

HBOI scientist dennis hanisak studing seagrass
Harbor Branch Oceanographic scientists survey seagrass restoration site, Banana River. Hint: The water, clouded with algae, is part of the problem.

Florida boasts the largest continuous seagrass meadows in the nation, totaling more than 2.2 million acres, each of which contributes an estimated $20,500 to the economy per year. The East Coast’s Indian River Lagoon is home to seven seagrass species, more than anywhere else in North America. Once the continent’s most biodiverse estuary, the lagoon annually adds an estimated $7.6 billion to Florida’s economy, largely thanks to the productivity of seagrass, historically its baseline organism.

In 2011, however, the first of a series of devastating phytoplankton blooms knocked the lagoon’s ecological balance off-kilter. Decades’ worth of nutrients from agriculture, homes, and wastewater supercharged the growth of naturally occurring microorganisms, causing them to coat the water’s surface and block light from reaching the seagrass below. The 2011 bloom alone slashed the lagoon’s 79,591 acres of seagrass to 45,730. Phytoplankton continue to take a toll. The results of St. Johns River Water Management District (SJRWMD) monitoring efforts estimate the lagoon’s 2021 acreage at 19,821 acres, down from 33,205 in 2019. The decline in grass has set off a chain of consequences for the lagoon’s wildlife, including last year’s unusually high number of manatee deaths.

According to one estimate, replacing just the amount of seagrass lost in the Indian River Lagoon from the 2011 superbloom would require one million units of seagrass to be planted every day for 52 years. Scientists agree that long-term restoration of seagrass ultimately hinges on improving water quality, a heavy lift that will take years. But they’re not resting on their laurels in the meantime. While seagrass replanting methods are still in development, what they learn from pilot projects such as the one at Samsons Island will help organizations and volunteers spring into action to plant seagrass at a larger scale when the lagoon is in a healthier state.

At this site, researchers from HBOI and Florida Oceanographic Society are testing two methods of planting shoal grass, the lagoon’s most widespread species. The grass is surrounded by a 75-foot-long oyster breakwater with sprinklings of clams. The hope is that the plants and animals can bolster one another’s survival and growth, Hanisak says. Seagrass benefits shellfish by increasing the water’s pH level and producing oxygen. The oysters, in turn, filter water and help protect the grass, which is particularly vulnerable in its early stages. Clams reduce sulfide levels harmful to seagrass. But Hanisak notes a breach in the surrounding fence. Animals are getting in and cropping the seagrass before it has matured into a lush, self-sustaining meadow.

Grazers such as manatees, turtles, and fish are just one of many challenges to giving seagrass a good start. Stingrays pockmark young meadows with pits, and lugworms tunnel holes in the sandy bottom. Today, the river is toffee-colored, with visibility limited to just a few inches, restricting the amount of light reaching the grass.

Still, Hanisak is heartened to see that shoal grass is expanding beyond the edges of the planted quadrants. He also spots the threadlike leaves of widgeon grass, Ruppia maritima, growing among the shoots, a sign that the meadow is naturally recruiting other seagrass species.


seagrass restoration area on volunteer day
Drone view of restoraton site.

Seagrasses are known as ecosystem engineers, shaping their surroundings into hospitable habitats for other life forms. They purify water, generate oxygen, stabilize the seafloor, store carbon, and serve as a natural coastal buffer, reducing wave energy by about 40 percent. HBOI research estimates that one acre of seagrass supports 40,000 fish and 50 million invertebrates, animals such as worms, crabs, sponges, shrimp, snails, and shellfish. Seagrasses also curb marine bacteria that threaten coral reefs and contaminate seafood. In Florida, seagrass acts as a vital nursery for an estimated 70 percent of the fish that anglers catch, including species such as spotted seatrout, grouper, and tarpon.

The complexity and diversity of seagrass meadows have prompted scientists such as Hanisak to equate them with rainforests, and they are considered the third-most valuable ecosystem in the world after estuaries and wetlands. Seagrasses grow in shallow salty or brackish water from the tropics to the Arctic, undergirding 20 percent of the world’s biggest fisheries. A 2019 study from the University of Florida showed that seagrass meadows can persist in the same place for hundreds and possibly thousands of years when growing conditions are right.

But seagrass is locked in a struggle for survival worldwide. According to a 2020 United Nations report, seagrass has been declining globally since the 1930s. Today, the equivalent of a football field is lost every 30 minutes. One billion people live within about 60 miles of seagrass meadows, exposing these marine plants to the effects of coastal development, pollutants, and freshwater discharges that disrupt the salinity, light, and nutrient levels they need to thrive. In Florida, the Indian River Lagoon and Florida Bay have suffered the worst seagrass losses over the past decade, but they are not alone. Water managers recently reported Tampa Bay lost about 16 percent of its seagrass, more than 6,350 acres, from 2018-2020. Seagrass acreage dropped 18 percent in Sarasota Bay and 23 percent in Charlotte Harbor during the same two-year period.

seagrass on sailfish flats in 2010
Shoals north of the St. Lucie Inlet, often called Sailfish Flats, were covered with seagrasses in December 2010 Google Image photo.
seagrass die off on sailfish flats 2017
By January 2017 Sailfish Flats is barren—and remain mostly so today.

Scientists often describe seagrass as suffering from a “charisma gap” compared with other coastal ecosystems. Only 26 percent of the planet’s known seagrass meadows fall within marine protected areas, compared with 40 percent of coral reefs and 43 percent of mangroves. For policymakers and much of the public, seagrasses can remain out of sight and out of mind and, as a result, fail to garner enough attention or conservation measures.

That could be changing, says Lori Morris, an environmental scientist at SJRWMD. While anglers have long been familiar with the crucial role seagrass plays in its environment, it’s gradually gaining a larger share of the public spotlight, fueled in part by a record number of manatee deaths. “I believe people are realizing what a resource it was,” Morris says. “They’re the slow-growing, stable part of the system that used to keep things under control.”


identify seagrasses

In Florida, seagrass acts as a vital nursery for an estimated 70 percent of the fish that anglers catch, including species such as spotted seatrout, grouper, and tarpon. Seagrasses can adapt to moderate changes in their environment, decreasing their growth rate and leaf size in shady conditions, and turbocharging in response to nutrients. Too much shade or nutrients, however, can prove lethal.


seagrass by depth
Diagram and seagrass illustrations from Integration and Application Network (, University of Maryland Center for Environmental Science.

Florida’s seagrass acreage may be shrinking at an alarming rate, but don’t mistake these plants for delicate lilies. They’re remarkably resilient, Hanisak says. Fewer than 0.05% of all plant species can survive—let alone flourish —in saltwater. A study by Morris showed that after being hit by back-to-back phytoplankton blooms in 2011 and 2012, seagrass in the Indian River Lagoon actually rebounded between 2013-2015 before another bloom erased its progress.

Seagrasses can adapt to moderate changes in their environment, decreasing their growth rate and leaf size in shady conditions, and turbocharging in response to nutrients. Too much shade or nutrients, however, can prove lethal.

While seagrasses are sometimes confused for seaweed, they’re actually more closely related to flowering plants on land, as well as other grasses and palms.

One of the primary challenges to restoring seagrass is its reproduction, which is frustratingly difficult to study, Hanisak says. The grasses can sexually reproduce, producing small flowers, seeds, and even tiny fruit, but it’s nearly impossible for scientists to catch them in the act. How seagrass flowers are pollinated remains poorly understood—possibly via currents or crustaceans.

turtle seagrass close up
Many species depend on healthy grassflats. Turtle grass pictured here.

However, seagrasses usually multiply by cloning themselves, spreading under the sediment and sending up shoots that have the same DNA as the parent plant.

This can pose a puzzle for scientists: If they transplant grass from existing meadows to colonize bald patches, are they really expanding total acreage?

“That’s just stealing from Peter to pay Paul, and you may be impacting the donor bed,” Hanisak says. “I think if you can grow seagrasses in a sustainable nursery—by sustainable, I mean once you get started, you harvest when you can, and you let your nursery grow back without having to grab any more plants—that’s kind of the goal.”

Each of Florida’s seven seagrass species has its own preferred growing conditions, requiring a certain amount of light, salinity, water depth, and pH. As coastal development, freshwater discharges and other human activities transform the state’s coastal ecosystems, seagrass diversity will likely shift, researchers say. Shoal grass, which has flat, blade-like leaves that grow to about half a foot tall, tolerates difficult growing conditions more than other seagrasses and could increasingly replace them over time, according to a study by Morris.

“The loss has decimated the seatrout, pinfish and other fishes, crabs and shrimp, creating areas devoid of marine life.” – Capt. Alan Sherman, Miami

Before the emergence of superblooms, damage from careless boaters was one of the primary threats to seagrass, Hanisak says. Scars caused by dragging anchors and engines divide meadows, leaving bare patches that take years to heal over. Turtle grass, Thalassia testudinum, can take 5-10 years to recover from a prop scar, while shoal grass can heal over in about a year or two, due to differences in growth habits.


spotted seatrout on seagrass flat
Spotted seatrout rely on seagrass habitat as juveniles, and adults like this one prey on pinfish and other organisms associated with grassbeds.

Anglers across the state have noticed dramatic changes in local fish populations as seagrass disappears and have had to adjust longstanding fishing habits as a result. Capt. Ray Markham has watched grass decline in the Tampa Bay area since 2018 due to red tide and pollution.

“Without suitable habitat, fish will leave and seek a better place,” Markham says. “The west side of Tampa Bay is dead for trout. From the St. Petersburg Pier south to Fort De Soto, I haven’t caught a trout since May of last year. I’m forced to cross the bay to fish or fish in upper Tampa Bay.”

According to Capt. Alan Sherman from Miami, it’s more of the same in Biscayne Bay: “The loss of 80% of our healthy shoal grass and manatee grass [Syringodium filiforme] that once covered the shallow flats of North Biscayne Bay and the west side of South Bay has decimated the seatrout, pinfish, and other bay fishes, crabs, and shrimp that once inhabited these areas, creating areas void of marine life. The result of this to my business has been disastrous, forcing me to look for different species to target for my clients.”


tailing redfish looking for crabs in turtle grass
Red drum tailing in turtle grass, abundant in some areas of Florida Bay—but subject to periodic dieoffs.

Capt. Paul Fafeita, an inshore fishing guide based in Fort Pierce and Vero Beach, says, “A lot of attention was brought to the almost total loss of seagrasses throughout most of the Indian River Lagoon this past year with over 1,000 manatee deaths. But for the last several years, the disappearance of nearly all the shoal grass, Johnson’s grass [Halophila johnsonii], widgeon grass, and more have all but collapsed the dependable inshore fisheries for speckled seatrout, snook, and redfish in the lagoon.”

Northern Indian River Lagoon guide Jim Ross describes shoal grass, widgeon grass, and manatee grass as “the lifeblood” of saltwater nurseries in the Indian and Banana Rivers and Mosquito Lagoon, supporting juvenile fish, crabs, and shrimp.

“Because these lagoons have virtually no tidal influence, the few oyster bars and limited undercut mangrove banks that are present do not provide enough cover for these animals to avoid extinction-level predation from larger fish, now that our seagrasses have been killed off by rampant human pollution,” Ross says.

Florida’s Southwest Coast has suffered less catastrophic seagrass losses than elsewhere in the state. But the abundance of local fish species has still decreased, according to Capt. Greg Stamper of Fort Myers.

“There are areas like the mouth of the Caloosahatchee where you no longer find suitable seagrass to fish,” Stamper says. “But in almost all areas, it seems there are fewer snook, reds, and trout due to the overall thinning of the seagrass throughout the entire area.”

Seagrass degradation doesn’t just impact inshore fish species. Grant Gilmore, senior scientist at Estuarine, Coastal and Ocean Science, Inc., documented robust populations of juvenile grouper, yellowtail, and mutton snapper along the shoreline a quarter-mile inside of the St. Lucie Inlet 15 years ago.

“It’s not just juvenile snook and seatrout that require shallow grass beds to survive,” Gilmore says. “Research indicates that grouper and snapper larvae gravitate to grass areas just inside inlets.”

One of the most important ways anglers can boost seagrass recovery is by using their voices, says Chuck Jacoby, supervising environmental scientist at SJRWMD. “Supporting efforts by whomever— cities, counties, state—to reduce loads of nutrients to the lagoon is a really positive effect. Take Brevard County, when they put on the sales tax [to fund lagoon restoration], the anglers were a big part of saying we should be doing this,” he says. “That kind of support is really critical because things won’t happen if people don’t vote for it.” FS

Published Florida Sportsman Magazine May 2022

Click here to see the next installation of the Seagrass series, Seagrass 102: 4 Ways You Can Help Restore Seagrass

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