An unusually large influx of gray whales into San Francisco Bay this year has thrilled boaters, beachgoers and tourists along Crissy Field, Angel Island and other shoreline locations, but the strange behavior and apparent poor condition of the magnificent sea creatures has marine biologists worried.

Four whales, all between 25 and 40 feet long, were spotted in the bay Thursday, a remarkable occurrence in any other year. But this year, it was merely the latest in a constant stream of leviathans entering the estuary since last month.

Whales have been seen in the bay every day since Feb. 17 and are hanging out there for long periods of time. The behavior is abnormal for a species that generally makes a beeline from Mexico for Alaska this time of year, and some believe it is indicative of a desperate search for food.

“Definitely it’s unusual,” said Bill Keener, a marine biologist with Golden Gate Cetacean Research, who identified one whale that has been hanging out in the bay for more than a month. “We see two or three a year come into the bay and stay a day or two. All of a sudden we have multiple whales.”

The whale bonanza isn’t necessarily a problem, according to marine biologists, but a major die-off occurred the last time scientists saw this many whales in the bay.

There have been other disturbing signs, too. The females arrived later than usual this season to the lagoons in Mexico, where they nested and gave birth to fewer calves than normal. More of them than average also died or appeared emaciated, according to researchers.

Then one of two whale carcasses found in the bay last week died of severe malnutrition, the Marine Mammal Center and California Academy of Sciences said. A cause of death could not be determined for the second. Both were 23-year-old females.

Researchers are afraid the whales are not finding enough food to sustain them through the year because the retreating ice fields at their feeding grounds in the Arctic are forcing them to swim farther to find prey. This, in turn, means they’re not fully nourished when they head south again, causing a lower birth rate and forcing the famished beasts to stop for snacks as they pass San Francisco again on their way north.

“In recent years, biologists have observed cases of young gray whales in poor body condition,” Dr. Padraig Duignan, the chief research pathologist at the mammal center, said in a statement after the necropsies. “This species faces the longest annual migration of any whale on Earth. It’s likely that after not feeding this winter,” the animals don’t have “enough reserves built up to survive” the journey north.

The situation is troubling, but a lot of whales cavorting in the bay doesn’t necessarily mean there is an emergency, said Frances Gulland, a marine biologist with the U.S. Marine Mammal Commission.

Gulland performed the two necropsies, which she said did not definitively point to a lack of food as the problem. The emaciated whale had entanglement scars, she said, meaning it could have starved as a result of being trapped in fishing gear. The other whale had a large propeller wound, she said.

“It could be an early warning or it could be a little blip. At this point, it’s not as if there are hundreds of thin whales dying of starvation,” Gulland said. “But I’m definitely on the alert. All the whale researchers should be paying attention and getting as much data as we can.”

The cetaceans, known as Eastern North Pacific Gray Whales, generally leave their breeding grounds in Baja California and migrate with their calves from Mexico to the Arctic between February and May. They generally don’t eat during the northern migration and then feed in Alaska throughout the summer before turning around for the return voyage between November and January.

Gray whales are one of conservation’s major success stories after being hunted almost to extinction over the past 200 years. A whaling station existed in Point Richmond until the 1960s.

There were only about 4,000 gray whales in existence in the 1930s, but, because of bans on whale hunting, the population has steadily rebounded since then. In 1999, there were 26,600, according to the National Marine Mammal Laboratory in Seattle, and then a huge die-off occurred.

In 1999 and 2000, the population declined about 20 percent, to 18,000. At least 40 dead gray whales were found on beaches in the Bay Area in those two years. The population has again recovered, and now there are an estimated 25,000 North Pacific grays, which is close to their historic population.

What is alarming some scientists is that the last time this many gray whales were seen entering the Golden Gate was in 1999, just when the big die-off was getting under way.

John Calambokidis, a senior research biologist with Cascadia Research in Olympia, Wash., said the population may have simply reached carrying capacity.

“We may be facing another situation where they have reached the limit of their food supply,” said Calambokidis, who added that an unusually large number of skinny whales have also been seen in Puget Sound. “This is the tail end of their seasonal fast, where they have not been eating for three or four months and they may be desperate.”

The big mammals clearly face many perils. They are often hit by ships — as many as 9,000 large vessels pass through the Golden Gate every year — or get entangled in fishing gear. Killer whales also patrol Monterey Bay and ambush mothers and their calves as the leviathans attempt to cross a deep-water canyon there.

The question is to what degree are human factors playing a role in limiting their food supply.

It has been well-documented that the Arctic ice has been retreating as a result of climate change. Scientists believe gray whales, which feed on the edge of the ice shelf, may have been forced to swim farther and cut short their feeding time because of it, thereby reducing the number of calves born the following year.

“I absolutely think it’s something we should be concerned about,” Calambokidis said. “Whenever you see an increased number of strandings, animals in unusual areas, animals in poor nutritional condition, these are things that we want to investigate.”

Peter Fimrite is a San Francisco Chronicle staff writer. Email: pfimrite@sfchronicle.com Twitter: @pfimrite