The stench of decaying algae began rising from coastal waterways in southeastern Florida early this month, shutting down businesses and beaches during a critical tourism season. Officials arrived, surveyed the toxic muck and declared states of emergency in four counties. Residents shook their heads, then their fists, organizing rallies and haranguing local officials.

In truth, there was little they could do: The disaster that engulfed the St. Lucie River and its estuary had been building for weeks. In May, a 33-square-mile algal bloom crept over Lake Okeechobee, the vast headwaters of the Everglades. After an unseasonably wet winter, the Army Corps of Engineers was forced to discharge water from the lake to lower water levels, flushing the ooze along channels to the west until it coagulated along the shores of the famed Treasure Coast.

The mess in Florida is only the latest in a string of algal blooms that some experts think are increasing in frequency and in severity. An immense plume of blue-green algae last September covered a 636-mile stretch of the Ohio River. A month earlier, the city of Toledo, Ohio, warned more than 400,000 residents to avoid drinking tap water after toxic algae spread over an intake in Lake Erie. (Indeed, the Lake Erie bloom is now an annual event.)

The largest and most dangerous algal bloom ever recorded, which ranged from Central California to British Columbia, produced high levels of a toxin that last year closed crab and clam fisheries along the West Coast.

Algae is a catchall term referring to a variety of aquatic organisms that generally rely on photosynthesis for energy and reproduction. Blue-green algae are cyanobacteria, for instance, while red tide is composed of tiny dinoflagellates. Seaweed is a sophisticated alga, as is kelp.

Blooms are a natural occurrence. According to William Cochlan, a senior research scientist at San Francisco State University, Native Americans for centuries knew to avoid bioluminescent water. Scientists would later discover that the glow was caused by dinoflagellates that also produce a hazardous neurotoxin.

Many algal species produce similar toxins. When vast blooms occur, these poisons can spread through the environment and up the food chain to fish and animals that feed on them. Cyanobacteria produce microcystins, for example, that can affect the liver and can be deadly to humans — one reason Toledo banned the drinking water.

Although they occur naturally, algal blooms are being intensified by human activity in ways that scientists are still trying to quantify. Chief among the culprits: runoff from farms, feedlots and municipal sewer systems.

“The bloom itself is the visual manifestation of nutrient overenrichment in lakes,” said Tim Davis, an ecologist at the National Oceanic and Atmospheric Agency’s Great Lakes Environmental Research Laboratory in Ann Arbor, Mich. “In freshwater systems, both nitrogen and phosphorus are the main nutrients.”

In Florida and the Great Lakes, nitrogen and phosphorus come mainly from fertilizers used in large farming operations, along with septic tanks, manure and stormwater. Scientists have been aware of the nutrient problem for decades: It is partly why phosphorus was removed from laundry detergents.

The vast algal bloom in the Pacific last year was also fed in part by El Niño, the mass of warm water that forms periodically off the West Coast. But longer-term climate change may also be playing a role, some experts say.

Warming atmospheric temperatures and wetter weather in some parts of the country increase the nutrient-laden runoff into streams, lakes and the ocean. And as ice melts in the Arctic, sea temperatures are rising and more sunlight is filtering into the ocean.

“Some of the features of climate change, such as warmer ocean temperatures and increased light availability through the loss of sea ice in the Arctic, are making conditions more favorable for phytoplankton growth — both toxic and nontoxic algae — in more regions and farther north,” Kathi Lefebvre, a biologist at NOAA’s Northwest Fisheries Science Center in Seattle, said.

“It is likely that toxic blooms will continue to increase and expand as these features of climate change continue,” she added.