In 19 years of piloting his boat around Lake Superior, Jody Estain had never observed the water change as it has this summer. The lake has been unusually balmy and cloudy, with thick mats of algae blanketing the shoreline.

“I have never seen it that warm,” said Mr. Estain, a former Coast Guard member who guides fishing, cave and kayak tours year-round. “Everybody was talking about it.”

But it was not just recreational observers along the shores of the lake who noticed the changes with concern. Lake Superior, the largest of the Great Lakes with more than 2,700 miles of shoreline, is the latest body of water to come under increased scrutiny by scientists after the appearance this summer of the largest mass of green, oozing algae ever detected on the lake.

From the Gulf Coast to the northernmost shores of the United States, scientists and government officials are working to decipher algae bloomsto help them interpret the causes of the blooms, changes to their climates, and the effects the blooms have on public health and regional environments.

Scientists generally agree that algae blooms are getting worse and more widespread, and are exacerbated by the warmer water, heat waves and extreme weather associated with climate change. They are also intensified by human activity, such as from farm and phosphorus runoff, leakage from sewer systems, and other pollution.

The problems that algae blooms pose to fresh and marine waters have been propelled to the forefront in recent years by high-profile events like the shutdown of the water supply in Toledo, Ohio, in 2014 after toxic algae formed over the city’s water-intake pipe in Lake Erie, as well as the production of a toxin by a species of algae off the West Coast in 2015.

Other areas, including the Finger Lakes in New York and Utah Lake south of Salt Lake City, have also experienced an unusually high number of blooms in recent years.

This week, the National Oceanic and Atmospheric Administration’s laboratory for environmental research on the Great Lakes warned that some parts of Lake Erie were not fit for recreational activities because of an algal bloom.

Starting in August in Lake Superior, reports of the thick, green algae stretching along about 50 miles of the southern shore reached Robert Sterner, the director of the Large Lakes Observatory at the University of Minnesota Duluth, and his team.

“We believe it to be the largest, most intense bloom yet,” he said. “I have been emphasizing we are talking about a small volume of Lake Superior, but it is a very highly prized, recreational part of the lake.”

Dr. Sterner said that while scientists did not completely understand the causes and frequency of blooms, they start with warmer water. And Lake Superior, he said, “is one of the fastest-warming lakes on earth.”

Algae blooms are a natural occurrence, but certain species can be toxic. While the species of algae found in Lake Superior can become toxic, Dr. Sterner said, tests showed that none of its commonly occurring toxins were found in hazardous concentrations.

Harmful algal blooms are a “national problem,” Donald M. Anderson, a senior scientist at the Woods Hole Oceanographic Institution, told the Senate Committee on Commerce, Science and Transportation in Washington on Tuesday.

“Their increasing frequency and intensity are impacting the economics and environmental health of communities, states, tribes and regions around the nation,” he testified.

In an interview on Wednesday, Dr. Anderson said that scientists were seeing outbreaks surging in places they had not appeared before.

“The fresh water problem has exploded in the United States,” he said. “But even on the marine side, we are seeing events larger in scale.”

Scientists and National Park Service employees were unaware of any noticeable blue-green algae blooms in Lake Superior before July 2012, when visitors reported surface scum along a 15-mile stretch of shore near the Apostle Islands, Dr. Sterner said.

That was after 10 inches of rain drenched the Duluth region, wrecking infrastructure and shooting a plume of sediment into the lake, Minnesota Public Radio reported this month in a feature about this summer’s algae blooms.

The latest algae bloom in Lake Superior arose after major storms in Junedumped nearly a foot of rain across the region, the report said.

In July, Mr. Estain noticed algae around the Apostle Islands, in the western part of the lake, and he said it took up to three weeks to break up, longer than usual.

Wisconsin’s Department of Natural Resources hosted an outreach event to inform the public about the potential health risks. National Park Service signs went up, amid warnings that the blooms were being tested for toxicity.

“We saw the formation of large green surface blooms of cyanobacteria,” said Brenda Lafrancois, a National Park Service ecologist, using the term for blue-green algae.

“The surface blooms are a concern for aesthetic reasons,” she said. “In the bigger picture, the concern is that the blooms might be a symptom of broader changes, like increases in nutrients and warmer temperatures.”

Dr. Sterner said his team had yet to “connect the dots” about the triggers for the Lake Superior algal bloom, but he noted a possible link to warmer temperatures.

“So we think we might be hitting some temperature threshold,” he said. “Something out there has changed, and the one thing we know securely is that the lake is warming.”