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Though tourists flock to Miami for its warm weather and pristine beaches, most don’t think about the unique ecology of adjacent Biscayne Bay. Shallow and clear, the bay is important for Miamians’ recreation and economy, but the brackish water and surrounding land are also home to thousands of species living in dozens of unique habitats. Covering an area of more than 225 square miles, the bay’s shores, waters, and the seabed grasses that live within them host hundreds of species of fish, crustaceans, and the more than 200 species of birds that feed on them. That includes the threatened Wood Stork, which hunts and nests in this habitat tucked just beneath the city.

But decades of urban development and pollution have left Biscayne Bay so vulnerable that the National Oceanic and Atmospheric Administration has named the region the country’s newest Habitat Focus Area, allowing seven Miami-area conservation groups and universities to coordinate a rescue.

A number of factors have contributed to the bay’s ecological unraveling. Destruction of the Everglades means that more freshwater reaches the bay than before, causing huge die-offs of saltwater organisms like shrimp. Construction upstream has wiped out many of the mangrove forests, which filtered out some water pollution and provided a haven for young fish. “We’ve been monitoring bird populations for 80 years in Biscayne Bay, and I can tell you it’s not a pretty picture,” says Laura Reynolds, the executive director of the in Miami.

Worst of all, the naturally calibrated nutrient exchange of the brackish bay is being thrown out of whack, leading to increasing algal blooms. Explosive colony blooms of the microscropic photic zone dwellers has long been a problem in the nearby Keys, where rampant algae growth is ignited by nutrient-rich agriculture runoff and waste slurries of the upstate phosphate industry. But recently they’ve begun to appear in even the most pristine of Biscayne’s waters, says , an ecologist at the NOAA’s Southeast Fisheries Science Center in Miami, adding that there’s a rush to solve the mystery of why.

Even if the why is murky, the how is depressingly clear. During a bloom, algae cloud the water, absorbing the sunlight that photosynthetic organisms need to survive. Nearly all the bird species living around Biscayne Bay feed near or in the water, says , the director of the and the chair of citizen science for the Tropical ���Ϲ��� Society. A big worry is that the puffs of green and red will smother the abundant marine life and cloud the diamond-clear brine—a disaster for hungry predators. “If hunters can’t see the prey below the surface,” says Galvez, “the effect will trickle up to all bird populations.”

Recognizing the looming catastrophe, NOAA designated the more than 225 square miles of mangrove forests and barrier islands that wreathe the bay’s shallow waters—and the grassy seabed within them—as the nation’s newest Habitat Focus Area. Local conservationists believe that NOAA has intervened at a critical moment for Biscayne Bay. By selecting the bay as a habitat focus area, NOAA will provide oversight and coordination between organizations working there, such as the Tropical ���Ϲ��� Society. With greater coordination between environmental organizations and more available funding, conservationists are optimistic that their timely intervention may be just enough to save the bay and the wildlife that lives there.

As co-leader of the , the overarching national program that names the focus areas, Browder and her colleagues hope to understand algal blooms before they have a permanent effect on Biscayne Bay. “We’re focusing on what might be the cause in more specific terms,” Browder explains. Organizations will dedicate more effort to monitoring the bay, identifying indicator species, and gathering enough information to recommend new policies to local and state governments.

NOAA hopes to see some progress in the next three to five years, Browder says, although the long-term implications of today’s projects won’t be apparent for many years to come. “Usually it takes longer than five years to know, ���Ϲ���’s Reynolds says, “but we’ll know we’re successful if we start to see the amount of vegetation increase, the fish come back, and then there are more birds roosting, nesting, and feeding.”

In spite of clear challenges, ecologists seem optimistic that it’s not too late to save Biscayne Bay. “It’s now or never,” says Browder. “Let’s look at Biscayne Bay now while we might be able to make a difference.”