A frightening number of sick and starving sea lion pups are turning up on California beaches this year, leaving scientists struggling to explain a third deadly winter for the pinnipeds.

Rescuers from San Diego to San Francisco Bay in January netted more than 250 frail pups, mostly 7-month-olds that should be nursing with their mothers in the Channel Islands or Mexico, not wallowing on the California mainland.

The number of sea lions taken into rehabilitation facilities this year exceeds the number of rescues during the same period in 2013, a year that prompted the National Marine Fisheries Service to declare a rare “unusual mortality event.”

“They just look very emaciated, very underweight,” said Erica Donnelly-Greenan, who manages the Sausalito-based Marine Mammal Center’s rescue station along Monterey Bay, where dozens of wayward pups have been found. “You can see the bones under their skin. You can get a visual of their ribs.”

The cause of the problem is unclear. Marine scientists say it may be warmer-than-average waters off the coast that are forcing mother sea lions in the Channel Islands to venture farther for food, leaving their young behind for too long.

“The pups are desperate and starving, so they just jump in the water and swim and get pulled to the coastline,” theorized Shawn Johnson, director of veterinary medicine for the Marine Mammal Center. “They’re just too small and too weak to dive and catch fish.”

The young sea lions normally don’t wean off their mothers until they’re 10 or 11 months old, Johnson said. That means the pups could struggle for survival for at least an additional three months. In 2013, more than 1,500 sea lions washed ashore, most over the first four months of the year.

“This is the third year that we’ve seen these mass die-offs, but this is the worst so far,” Johnson said. “If this continues, there will be some long-term effects on the sea lion population.”

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Fortunately, California sea lions have been relatively healthy in recent decades. Passage of the Marine Mammal Protection Act in 1972 helped boost their numbers after the animal was hunted for its hide and blubber for centuries.

The population is estimated at 300,000 today, according to the National Oceanic and Atmospheric Administration. Sea lions are common up and down the West Coast, typically breeding in the Channel Islands and south to Mexico, and spending the rest of their time on beaches and man-made wharves as far north as British Colombia. San Francisco’s Pier 39 has become a roosting point popular with sea lions, which draw camera-toting tourists.

Justin Viezbicke, stranding network coordinator for NOAA Fisheries in California, said it’s possible that sea lion numbers have hit a natural ceiling, with not enough food or habitat to support more animals.

“Has the population reached its capacity in the environment?” he said.

NOAA is also studying whether the recent die-offs may be linked to changing ocean conditions or some other problem at sea. Disease is not thought to be the issue.

“These animals are a puzzle piece for us,” Viezbicke said. “They provide insight into what’s going on in the environment. … These things could come back and affect humans.”

A team of NOAA scientists is monitoring mother sea lions on the Channel Islands in search of clues to what’s happening to their young.

The high numbers of sick pups have put rescue centers in a pinch as they struggle to get enough volunteers to collect the animals off beaches and find sufficient funds for food and treatment.

The Marine Mammal Center’s rehab facility in Sausalito is holding about 100 sea lions, many more than the dozen or so they typically have this time of year, officials there said.

The sea lions are being nourished with herring, often force-fed with tubes when they can’t ingest the fish on their own, and are being treated with antibiotics.

Kurtis Alexander is a San Francisco Chronicle staff writer. E-mail: kalexander@sfchronicle.com Twitter: @kurtisalexander

How to help

The Marine Mammal Center in Sausalito is collecting donations for food and treatment for sea lion pups that have been stranded on California beaches. Donations can be made at the center’s website: www.marinemammalcenter.org. The center can be reached at (415) 289-7325.