They’re back.

For the second straight year, humpback whales are finding their way into San Francisco Bay in large numbers and causing quite a stir.

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Rare sight: Whale shark, largest shark in the world, surprises local spearfisherman off California coast With a large number of humpbacks offshore, some are following prey — primarily anchovies — on high tides into the bay, where the whales have been seen jumping out of the water or “breaching.”

“One even made it as far as Racoon Strait off of Tiburon,” said Corte Madera resident Bill Keener, a researcher with Golden Gate Cetacean Research, who has snapped several photos of the whales from the Golden Gate Bridge. “But we see them mostly between the Golden Gate Bridge and Alcatraz. These guys are coming in for a purpose and that is feeding. You can see the anchovies jumping out of the way.”

While a spectacle, there is some concern for boater safety and the whales themselves. One kiteboarder crossed paths with a humpback and posted the video online.

The humpbacks are migrating north and for some, the food-rich coastal waters off Marin are a final destination for the summer before they head south to Mexico and beyond for the winter. Last month, scientists on the Farallon Islands off San Francisco counted 216 humpback whales over a period of more than two hours.

“The super abundance of food is due to the nutrient-rich, upwelled waters flowing down-current … carrying plankton on which fish, marine invertebrates, seabirds and other marine life feed; they act like a wellspring generating a rich food web,” said Mary Jane Schramm, spokeswoman for the Gulf of the Farallones National Marine Sanctuary.

Keener said up to 15 of the whales have been spotted in and around the Golden Gate and bay at any one time. Whales have come into the bay before, but the activity appears to have been rare until the past two years.

“It seems like the humpbacks have figured it out,” said Keener, who was able to identify some of the same whales who came into the bay last year. Last year most of the whales had left by August.

The whales can weigh as much 40 tons — 80,000 pounds — and newborns weigh about a ton. They measure up to 60 feet with females larger than males, and live about 50 years. Aside from anchovy and other small fish, the whales eat krill and plankton. They can eat up to 3,000 pounds of food per day. About 1,400 humpbacks feed along the California coast in the summer and fall.

In June 1970 humpbacks were designated as endangered under the Endangered Species Conservation Act after the species was hunted for decades. In 1973, the Endangered Species Act replaced the conservation act and continued to list humpbacks as endangered. But populations have rebounded.

The large mammals have always had a lore about them firmly established by Herman Melville’s epic “Moby Dick,” and helped along the way in popular culture in such stories as Walt Disney’s “Pinocchio” and the real-life drama of “Humphrey the Humpback” whale, who had bay visits in 1985 and 1990.

In May 2007 mother and calf whales “Dawn” and “Delta” were spotted far up the Delta and a massive operation was launched to rescue the whales that swam 90 miles inland. After a 10-day effort that involved playing recordings of other whales, surrounding them with boats, blasting them with fire hoses and banging on metal pipes dangling beneath the water, the pair eventually found their way out of the bay and into the Pacific. They made an appearance in Paradise Cay off of Tiburon, churning up mud as they left.