This is Sarasota Bay today, a 52-square-mile gem whose tattered beauty helps draw millions of visitors to the region every year.

A hundred years ago, Sarasota Bay attracted the area’s earliest settlers not with its beauty but with its amazing bounty. “The water appeared alive with multitudes of fish of every kind and little exertion was required to net as many as we wished,” an Army officer wrote back then. “Seafowl lined the beach, shown brilliantly in the sun from the red plumage of the flamingos and pink curlew.... Sharks were very numerous here, actually swimming about in schools. Any quantity of shellfish was to be had.”

Sarasota Bay still stretches about 56 miles from Anna Maria Sound to the Venice Inlet, just as it has for generations. But those settlers might have a hard time recognizing it these days, now that half a million people live here.

The scattered salt marshes that once covered the miles between the bay and the Myakka River are a distant memory, drained by the early farmers. About 40 percent of the mangroves that once ringed the bay—crucial habitat for the fish and other marine creatures that called it home—were wiped out between 1880 and 1990 to accommodate waterfront development. And more than 100 miles of seawalls and other hardened shore structures now dominate the shoreline, making what was once a fluid and naturally evolving landscape into a hard and lifeless barrier.

In just the past 30 years, throughout the bay’s watershed—the 150-square-mile area where water flows downhill into the bay through such waterways as Whitaker Bayou and Phillippi Creek—more than a third of the forested freshwater wetlands have been wiped out. Wetlands filter out water pollution, so now that they’re gone, every hard rain carries down to the bay a fresh load of fertilizer and pesticides from lawns and golf courses.

The consequences of all this degradation have long been obvious to people like Tom Mayer, a Longboat Key native who has worked around the bay for 35 years. “A lot of people moved in, and the nature moved out,” says Mayer, a professional mangrove trimmer. Newcomers see a flock of ibis pecking at their lawns and think there’s plenty of wildlife still around and the bay is all right, he says. They don’t realize that the birds are in their yard “because somebody developed where they used to be.”

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The first visitors to what is now Sarasota were fishermen looking for a big catch. Even 50 years ago, when fewer than 20,000 people lived in Sarasota, the bay’s sand flats held a multitude of clams and the sea grass beds were thick with scallops and oysters.

Cortez fish-house owner Karen Bell says her father used to tell her stories about netting a boatload of fish one day “and they would come back a few days later and catch even more,” she recalls.

These days the fish aren’t nearly as plentiful as they were back then. One big reason: A wealthy aluminum magnate named Arthur Vining Davis.

As the longtime head of the Alcoa aluminum company, 80-year-old Davis was already one of the nation’s wealthiest men when he retired to Florida in 1948. But he just couldn’t resist the lure of making even more money in real estate. So he founded Arvida, combining the first two letters of his three names to give it his personal stamp, and bought up land all over South Florida that he believed to be ripe for development. Among his acquisitions: the southern half of Longboat Key, most of Lido and all of Bird, Otter and Coon keys in Sarasota Bay, purchased for $13.5 million from circus titan John Ringling’s estate.

Bird Key was Arvida’s first target in Sarasota, a 14-acre island that had already been boosted with 30,000 cubic yards of sand dredged up from the bay by its first owner back in 1912. Ringling himself had built a causeway across Bird Key to get customers over to the waterfront homesites he was selling on St. Armands Key.

Although there were other attempts to develop the key, not until Davis came along to push it through did any succeed, in part because city officials were concerned about the effects on the bay. But Davis convinced them to give him a green light. He dredged up enough of the bay bottom to create 511 homesites, 291 of them classified as waterfront since they sat on a series of finger canals. The first homes went on sale in 1960 for up to $32,000. (Now those homesites are worth millions.)

Davis was far from alone. Dredge-and-fill operations in the 1950s and 1960s wiped out more than 1,800 acres of the bay’s coastal wetlands and nearly 4,500 acres of bay bottom to create waterfront homes, helping to destroy 30 percent of the seagrass beds that provide food and shelter for most of the bay’s marine life.

Not long after Davis’ death at age 95, though, public attitudes changed. In 1967, when Arvida announced plans to fill more than 170 acres of submerged land around Otter and South Lido keys, a group called Save Our Bays formed.

When word got out in January 1968 that the head of Arvida was having lunch with Gov. Claude Kirk at the Bird Key Yacht Club, Save Our Bays mobilized a flotilla of more than 200 boats and yachts of all sizes to ring the bay area to be developed, blowing horns, whistles, and bells to show their displeasure. A month later, the Sarasota City Commission voted unanimously to reject the dredging project in order preserve the bay’s marine life.

Still, the dredging done for Bird Key, the Intracoastal Waterway and other alterations to the bay did plenty of damage, both direct and indirect. The water clouded up and seagrasses died. “The fishing was really bad then,” recalls Jonnie Walker, a longtime fishing guide on the bay.

Nevertheless, people kept flocking to buy houses around Sarasota Bay. They weren’t as interested in the bay’s health as they were in how it looked from their back yard.

Not long ago, a study found that the main way most residents use the bay is not for boating or fishing but as a scenic backdrop, notes Jono Miller, a New College professor and long-time environmental activist. But Walker says he isn’t sure the folks who have spent millions of dollars on a waterfront view even notice the bay anymore.

“I see a lot of houses where I never see any people outside,” the fishing guide says. “People pay an exorbitant price for that view and never enjoy it. They never look outside. They don’t care if it has any fish in it. Maybe if it stunk real bad, then they’d care about it.”

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Every afternoon, Karen Bell steps out of her fish house and looks at the bay. “I go out and look at the sunset,” she says. “It’s lovely, with the silhouettes of all the boats.”

Seven years ago, Bell and other Cortez residents pooled their resources in a bid to guarantee that the sunset view would remain for future generations. They bought 95 acres of land on the bay, 72 acres of it still covered in mangroves, to make sure it would stay undeveloped. The mangroves have been so reliable a source of young fish that locals have long called this area “the kitchen.”

The rest of the bay has not been so well preserved. Starting back in 1910, Sarasota city officials mandated that every waterfront home should have a seawall, and now little of the bay still has a natural shoreline. An EPA study five years ago found the bay is now constrained by more than 100 miles of seawalls.

Around the time the city first declared its preference for seawalls, its citizens voted to build a combination water and sewer system. The only problem was where the sewage eventually wound up: the bay. And Sarasota wasn’t the only one using the bay as a dumping ground. In times of heavy rains, Manatee County allowed partially treated sewage to flow into the bay as well.

By the 1980s, the bay had hit its lowest point. Because of all the pollution, parts of the bay suffered from major algae blooms. The blooms not only sucked oxygen out of the water, killing fish—they also blocked sunlight from getting to the remaining seagrass beds, killing them as well. Stimulating the bloom’s growth was a pollutant called nitrogen. So much nitrogen was pouring into the bay that tests showed it had hit 400 times the bay’s own natural level.

Federal and state regulators ordered a halt to the sewage dumping. Meanwhile, then-Congressman Porter Goss helped get legislation passed declaring Sarasota Bay a priority for cleanup under a new federal program. Thus was born the Sarasota Bay Estuary Program, created with the seemingly impossible mission of cleaning up a mess 200 years in the making.

The first step, improving the sewage treatment systems, has cost $200 million so far in state and federal money, says Mark Alderson, executive director of the Sarasota Bay Estuary Program. The county is spending another $150 million a year on the septic tank and package plant replacement through 2012. And the job is far from over. As the region developed, builders constructed 117 small—and often poorly built—sewer plants to deal with the waste from their subdivisions, while others relied on leaky septic tanks. County officials have managed to eliminate about 100 of those package plants and get rid of most of the septic tanks by extending sewer lines to those areas, Alderson says.

Eliminating the sewage dumping cut in half the nitrogen levels in the bay, Alderson adds. With less nitrogen to spur algae blooms, the water is clearer; and as a result aerial photos show that more than 500 acres of seagrasses have come back, helping to revive the fish population. “The clarity of the bay has improved a lot,” says Walker, the fishing guide.

Dealing with the seawalls and the polluted runoff, though, has not been as easy. Tearing out the seawalls would threaten to erode expensive private property. So instead the estuary program, working with Mote Marine Laboratory, has developed artificial reefs that can be planted near the walls and help them to function more as the mangroves did, providing a nursery for juvenile fish. A Mote study found more than 400 juvenile fish, including pinfish, silver perch, gray snapper, and sheepshead at one such reef installation, while at another seawall without the reef there were none, Alderson says.

But the U.S. Army Corps of Engineers has balked at issuing federal permits to employ the artificial reef attachments throughout the bay for fear they will be a hazard to boaters, according to Alderson. So for now, many of the seawalls remain as sterile as they have been for generations.

Although halting the flow of sewage into the bay eliminated half of the nitrogen pollution, what was left was still 200 times the bay’s natural level—and now most of that was coming from stormwater runoff. A major contributor to nitrogen pollution in runoff is the fertilizer put out on lawns, golf courses and landscaping.

“A lot of people are putting too much fertilizer out there, and we really don’t need it,” Alderson says. “If you’re over-applying it, there’s a good chance it’s not being taken up by the turf or ornamentals, and it’s winding up in the bay.”

State regulations that halt other kinds of pollution in stormwater runoff don’t address nitrogen. Meanwhile, a massive red tide bloom in 2005 wiped out many of the gains in the bay’s fish population. So many fish were killed that the bay’s hungry dolphins, deprived of their usual prey, began trying to steal anglers’ bait. Two became tangled in fishing gear and died.

There is no proven scientific link between polluted runoff and red tide, but the suspicion that the runoff at least fuels the blooms once they begin led to a sense of urgency in addressing the pollution problem. So Sarasota County officials put together a task force to draw up local regulations on fertilizer.