At island rookeries off the coast, 45% of the pups born in June have died, said Sharon Melin, a wildlife biologist for the National Marine Fisheries Service based in Seattle. Normally, less than one-third of the pups would die.
It's gotten so bad in the past two weeks that the National Oceanic and Atmospheric Administration (NOAA) declared an "unusual mortality event." That will allow more scientists to join the search for the cause, Melin said.
Pups are normally weaned from their mothers in April.
Even the pups that are making it are markedly underweight, Melin said.
The most recent pups weighed at the breeding area on San Miguel Island were about 16.8kg, Melin said. They should weigh up to 26.7kg by now, she said.
Melin said she doesn't know how the pups are making it to the mainland, but they must be using currents and swimming.
"That's a long way, and they are very small," she said. "They don't have a lot of fat, and the water is pretty cold. They are often dehydrated, which is typical with emaciation. It puts them in pretty bad condition."
Those landing on the mainland may have been looking for food if their mother stayed out foraging too long, Melin said.
Live sea lion strandings are nearly three times higher than the historical average, said Jim Milbury of the National Marine Fisheries Service, part of NOAA.
Between 1 January and 24 March, 948 pups were rescued, Milbury said. The bulk of those were in Los Angeles County, which had 395, followed by San Diego, Orange, Santa Barbara and Ventura counties, he said.
Last year, only about 100 pups needed saving during the same period.
At the Pacific Marine Mammal Care Centre in Laguna Beach, there were 139 animals being cared for Friday.
Of those, 131 were sea lion pups, said spokesperson Melissa Sciacca. She said the centre has treated more than 220 sea lion pups so far this year, while the centre treated 118 in all of 2012.
Southern California rescue facilities have become so crowded they have had to start sending pups to Northern California, said Jeff Boehm, executive director at The Marine Mammal Centre in Sausalito, which was caring for 30 starving pups.
Limited food supply
Scientists were performing tests to determine if the problem is food availability, disease or both.
Biologists knew last spring that this year's supply of anchovies and sardines could be limited, Boehm said.
"These two species of fish are an extremely important part of California sea lions' diets, and females simply may not have been able to nurse their young sufficiently, resulting in abandonment, premature weaning and subsequent strandings," he said.
Besides anchovies and sardines, sea lions also eat squid and other ocean creatures. Routine testing of seafood is being done by state and federal agencies and consumer safety experts are working with NOAA to find the problem.
"No link has been established at this time between these sea lion strandings and any potential seafood safety issues," NOAA said in a statement.
There has been no sign of adult female mortality, Melin said. But the pups' situation on the beaches is so bad, rescuers have had to leave the worst of them in an effort to save the strongest ones, she said.
Scientists expect the death toll to rise in April when weaning is supposed to take place. They also expect it to move further north, Melin said.
Anyone who sees a stranded sea lion, dead or alive, is asked to call the nearest marine mammal centre. Authorities say people should not touch the animal or let a pet near it, because sea lions can bite.