Deaths of Manatees, Dolphins and Pelicans Point to Estuary at Risk Rene Aldrin Capulong for The New York Times In Merritt Island, Fla., biological scientists use nets to capture and record data on fish. MELBOURNE, Fla. - The first hint that something was amiss here, in the shallow lagoons and brackish streams that buffer inland Florida from the Atlantic's salt water, came last summer in the Banana River, just south of Kennedy Space Center. Three manatees - the languid, plant-munching, over-upholstered mammals known as sea cows - died suddenly and inexplicably, one after another, in a spot where deaths were rare. A year later, the inquiry into those deaths has become a cross-species murder mystery, a trail of hundreds of deaths across one-third of the Indian River estuary, one of the richest marine ecosystems in the continental United States. Along 50 miles of northern estuary waters off Brevard County and the Kennedy space complex, about 280 manatees have died in the last 12 months, 109 of them in the same sudden manner as the Banana River victims. As the manatee deaths peaked this spring, hundreds of pelicans began dying along the same stretch of water, followed this summer by scores of bottlenose dolphins. The cause continues to evade easy explanation. But a central question is whether the deaths are symptoms of something more ominous: the collapse of the natural balance that sustains the 156-mile estuary's northern reaches. "We may have reached a tipping point," said Troy Rice, who directs the Indian River Lagoon National Estuary Program, a federal, state and local government partnership at the St. Johns River Water Management District. Mr. Rice's fear, widely shared, is that an ecosystem that supports more than 4,300 species of wildlife - and commercial fisheries, tourism and other businesses generating nearly $4 billion annually - is buckling under the strain of decades of pollution generated by coastal Florida's explosive development. The evidence of decline is compelling. In 2011 and 2012, unprecedented blooms of algae blanketed the estuary's northern reaches for months, killing vast fields of underwater sea grass that are the building blocks of the estuary ecosystem. The grasses are breeding grounds for fish, cover from predators, home to countless creatures at the bottom of the food chain and, not least of all, the favorite menu item of manatees. The sea grass has largely been supplanted by macroalgae, fast-growing seaweeds that clump into huge mats that drift free in the waters. And the character of the estuary is changing: already, algae-eating fish like menhaden are significantly increasing, Mr. Rice said. Leesa Souto, a conservation biologist who heads the Marine Resources Council, a nonprofit group devoted to protecting the estuary, quoted one expert as saying that the loss of grasses destroyed the habitat for 1.4 billion immature fish. "We fear the fishery collapse may be forthcoming as these missing juveniles will never reach adulthood two or three years from now," she wrote in an e-mail. The scope and suddenness of the algae blooms took scientists by surprise, but their source is no secret: off Brevard County, the estuary is badly overloaded with nitrogen, an essential plant nutrient found in fertilizers, rotting organic matter and human and animal waste. State and federal authorities long ago limited dumping of nitrogen-rich effluents from sewage-treatment plants and factories. But so-called nonpoint sources of pollution, like lawn fertilizer and septic tanks, have been far harder to control. Now, some experts say, the rapid urbanization of the Florida coast, from the boom years of the space age to the later growth of retirement condos, appears to have pushed the accumulation of those wastes. Brevard has grown explosively, to nearly 545,000 in the 2010 census, from 23,700 people in 1950. The Banana River and other fingers of the estuary are a bricolage of pristine nature reserves cheek-to-jowl with beachfront motels, tract homes fronting on canals, even a golf course in the center of the Banana River itself.