Seagrass keeps dying in Biscayne Bay. Is it getting too sick to recover?

Something is wrong in the north end of Biscayne Bay, where — despite decades of dredging and boat traffic and polluted stormwater runoff — thick meadows of seagrass once kept water gin clear and filled with marine life.

Nearly half the basin’s manatee grass has died. Many of the fish have fled. And on windy days, or with every passing Cigarette boat, mud swirls up from the bottom. It’s essentially a dust bowl, only underwater.

Ben Mostkoff, who has lived within blocks of the bay for nearly six decades, has watched the die-off spread, turning large swaths lifeless in what not long ago was a favorite inshore snorkeling spot.

“This entire basin was so clear that on rough days when we would want to go out boating and it was too rough, we would come in here,” said Mostkoff, a former Miami-Dade County ecologist who started the county’s artificial reef program. The waters were filled with “tarpon, snook, snapper, lots of grunt, even tropical fish on the ledges and sea trout. All kinds of sea trout. And manatees would be in here as well.”

Biscayne Bay’s shrinking seagrass bed

Use the slider to see how much Biscayne Bay’s seagrass footprint — the dark area in the bay — shrank from 2011 (left) to 2016 (right).Google Earth

The decline of the shallow basin between the Julia Tuttle and 79th Street causeways is just the latest sign of trouble for the urban bay. Beginning in about 2005, after twin hurricanes pounded South Florida, problems started popping up all over: a persistent algae bloom in the central section coated seagrass with macroalgae not found anywhere else in the bay; disappearing coral and sponges killed off by a toxic blue-green bloom at the less developed southern end; and shrinking fish populations just about everywhere.

By one measure — an ongoing study by county biologists discussed this week at a regional science conference — Biscayne Bay has lost more than 21 square miles of sea-grass over the past decade. That’s an expanse bigger than city of Miami Beach.

What’s driving the latest die-off in Tuttle basin remains open to speculation. Dan Kipnis, a fishing boat skipper turned environmental and climate advocate, believes it might be related to the recent filling of old dredge pits, which was meant to correct earlier damage but clouded water and likely altered water chemistry. Or it could be the usual suspects that have worsened water quality across the bay: aging leaky septic systems, water flowing from dirty canals filled with high levels of nutrients that don’t jibe with the bay’s need for low phosphorus levels; or periods of drought followed by heavy rain that upset salinity.

The biggest new X factor for some scientists could be the increased pumping of untreated stormwater from Miami Beach. The city has installed a massive pumping system that filters out large debris and oil but does nothing to treat nutrients like fertilizer or dog poop from yards or human waste from leaky sewer pipes.

Or perhaps it’s some combination of any or all the above, said Gary Milano, a former biologist with the county’s environmental department.

“It could be five different things and one of the things is the breaking point,” he said. “It’s death from a thousand cuts.”

Efforts are now underway to launch a rescue mission. County environmental regulators are finishing up a study to present to commissioners. And advocates are sounding alarms. On Saturday, the 35th annual Baynanza cleanup was held, possibly generating more attention and reminding the people who live around the bay what might be lost, and what needs to be done as South Florida wrestles with impacts from climate change.

“Whatever it is, once [seagrass] starts to die, it’s like a catalyst and it just keeps perpetuating itself,” said Susan Markley, who served as the county’s natural resources division chief and retired in 2014. “My own feeling is Biscayne Bay, like Florida Bay, is kind of on the knife’s edge.”

Perhaps because it so urban, the conditions in the bay have received little attention, compared to even-worse problems in Florida Bay, the Indian River and and other algae-plagued coastal waters farther up the coast. But among environmentalists, local regulators, the marine industry and business interests in Miami-Dade, there is growing concern that too little is being done to assess and address the problems — beginning with the basic step of monitoring changes in water quality in the bay.

The South Florida Water Management District, amid ongoing budget cuts, eliminated about 30 percent of the bay’s monitoring stations in 2014, leaving the county to scramble to find money to maintain both water quality monitoring and seagrass tracking. Efforts to track the effects of the beach’s pumps are still in the works.

In January, the Miami-Dade County Chamber of Commerce convened a panel of experts to educate business leaders on the growing woes. The National Oceanic and Atmospheric Administration, fearful that the bay had reached a “tipping point,” also designated the bay a special focus area to corral its resources in 2014. But so far, funding has been limited, said Joan Browder, the NOAA biologist based on Virginia Key serving as chief investigator on the project.

Earlier this year, Browder applied for more funding, but it’s unclear whether NOAA, which has been targeted by the administration of President Donald Trump for cuts, will follow through.

“There’s all this richness around us and a lot of it is dependent on Biscayne Bay — the real estate, the tourism, the restaurants,” she said. “Yet there is not very much money being spent to protect the bay. It’s like using a resource but not doing anything to keep it perpetuating.”

Its bounty can get easily overlooked in the hubbub surrounding it. The seagrass beds, that stretch 50 miles in NOAA’s study area from Dumfoundling Bay near Aventura to Barnes Sound near the Card Sound bridge, are among the planet’s largest continuous beds. In a 2013 study, researchers at NOAA, Florida International University and the University of Miami found the beds comparable to meadows around Australia’s world-renowned Great Barrier reef, with at least seven different grasses. They play a key part in keeping the whole coast healthy, providing nursery space for baby fish and habitat for shrimp and other little crustaceans, that lure bigger fish, like snapper, sea trout, snook, bonefish and tarpon.

And those draw an even bigger catch — a commercial fishing fleet, deep-pocketed anglers, divers, boaters and a recreational marine industry valued at $12.7 billion, according to a 2014 Florida Sea Grant study.

The bay has been beaten down before — and rebounded — but it happened only with a serious investment in monitoring and regulation.

Over the years, acres of bay bottom had been dredged to provide fill for causeways and nearly 20 artificial islands. Deep trenches crisscrossed parts of the bay. Untreated stormwater and sewage also flowed freely from the Miami River, the Little River, canals and waste systems. The historic flow of freshwater from the Everglades had also largely been cut off by development and flood control structures.

By the 1970s alarms were sounding. Florida designated the bay a marine preserve from the Oleta River to Card Sound. Activists began pushing to expand Biscayne National Monument, created in 1968 as development pressure mounted, into a full-fledged national park. Miami-Dade, which elected its leaders from countywide seats back then, also declared the entire bay a county park. At the time, it seemed like the whole county had a stake in its well-being.

“Unlike a lot of big estuarine systems in our state or even other parts of the country, almost all of Biscayne Bay is in the jurisdiction of Miami-Dade County,” Markely said. “All the commissioners were elected county-wide, so they all had that big picture perspective.”

Regulators also upped monitoring, with the county ordering an exhaustive physical that tried to measure vital signs: what lived on the bay bottom, the size of the seagrass beds, the number and kind of fish, shrimps and crabs, and the speed and direction of currents to determine how basins flushed. The county, and later state water managers, also set up a network of monitoring stations, mostly on the west side, to keep an eye on water conditions flowing out of canals and off land, Markley said.

All that information was then used to come up with a plan to improve water quality and bottom conditions in the bay. And the Tuttle basin thrived — at least until the seagrass started disappearing, a trend first noted in 2013.

“You could see every blade of grass, every little fish swimming around,” said Kipnis, the fishing guide.

It’s not that way now. Whatever the cause, the seagrass beds in Tuttle basin have shrunk and large parts of the bay elsewhere are now covered in macro algae, which doesn’t support anywhere near the marine life of a healthy seagrass. The bottom growth resembles seaweed and it can smother, and quickly replace, seagrass.

“It rolls along until it hits something like seagrass and then, if conditions are right, it starts explosively growing,” said Craig Grossenbacher, who heads Miami-Dade’s Natural Resources Planning section, which is in the midst of investigating the Tuttle basin die-off.

Water quality problems plague many of South Florida’s coastal waters. Rivers and estuaries on both sides of the coast have been repeatedly hammered by the release of excess, nutrient-laden water from Lake Okeechobee. The Indian River Lagoon, stretching along a handful of East Coast counties, has been in a downward spiral for decades, hit by multiple algae blooms and dolphin deaths. Florida Bay, the backyard of the Florida Keys and coastal Everglades, has cycled through a series of seagrass die-offs and algae blooms, which scientists largely blame on the reduction of historic freshwater flow from the Everglades.

A push this year by Senate President Joe Negron to speed up a key piece of Everglades restoration — a 60,000-acre reservoir that would have delivered more freshwater — was dramatically scaled back to just 14,000 acres. If approved by the Legislature and Gov. Rick Scott, it could provide some relief in coming years from Lake O pollution for the St. Lucie, Caloosahatchee and Indian rivers upstate.

But the project doesn’t promise much water or help for the southern end of the Everglades system — particularly for Biscayne Bay.

Advocates for the bay say Biscayne projects have often been put on the back burner in Everglades restoration plans or been repeatedly scaled back. Under Scott, money for research and water monitoring also has dried up. His administration has slashed spending on environmental issues, trimming the Department of Environmental Protection and calling water management districts to cut taxes for the past five years. In the cost-cutting, the South Florida Water Management District slashed $243,435 to pay for 20 stations in Biscayne Bay.

The district did not respond Thursday to a call for comment.

“There did seem to be a loss of political will to continue the monitoring because it’s expensive,” said biologist Jim Fourqurean, a seagrass expert at Florida International University.

The worry, said Markley, is that because so much of the coast surrounding the bay has been developed, state and federal environmental agencies may consider problems — like treating stormwater — too expensive or difficult to fix.

She doesn’t expect the bay to be socked with that “horrible green slime” that has fouled the Indian and St. Lucie river after Lake O dumping. But gin clear waters in Tuttle basin could be a thing of the past unless more resources are quickly put into figuring out what’s going and how to stop it.

“This is like eyes wide shut,” said Mostkoff. “Everybody is seeing what’s happening and not reacting.”

An earlier version of this story reported that Miami-Dade County stopped monitoring seagrass after the South Florida Water Management District cut funding. The county later used money from its general fund to continue efforts.

Follow Jenny Staletovich on Twitter @jenstaletovich

On Saturday, Miami-Dade County will host its 35th annual baywide Baynanza to clean up Biscayne Bay at 21 locations around the bay. To find out more, go to: http://www.miamidade.gov/environment/baynanza.asp.