The population of California sea otters, a species whose painfully slow recovery from near extinction has been as baffling as it has been disturbing, is nearly the same as it was last year despite intensive efforts to bring the frolicsome marine mammals back from the brink.

The U.S. Geological Survey counted 2,944 otters and pups along the California coast this year, about the same as the 2,939 that were seen last year. Most scientists agree that the number of animals, which are also known as southern sea otters, should be increasing, but hungry predators and a lack of food may be limiting their growth.

“The recovery of the California sea otter has stalled,” said Steve Shimek, executive director of the Otter Project, one of California’s sea otter recovery programs. “This is bad news. ... We must redouble our efforts.”

The beloved otter, whose luscious coat was so coveted by fur traders that the species was nearly wiped out, has pretty much been holding steady in its West Coast sanctum for about a decade despite intensive efforts to increase the population. One problem, marine biologists say, is an alarming uptick in shark attacks.

Jim Curland, advocacy program director for the nonprofit Friends of the Sea Otter, said 340 dead sea otters were found last year, many of them victims of great white sharks.

“That’s greater than 10 percent of the population,” Curland said, “so if mortality continues to be that high, it is going to be hard for them to recover.”

Toxins, boat strikes, gunshot wounds and disease have also played a part in keeping the population down, but lack of food may also be playing a significant role, said Tim Tinker, a biologist with the Geological Survey’s western ecological research center.

Mortality rate rises

“We are seeing elevated mortality suggestive of food resource limitation in some parts of the range, and increasing mortality from white shark attacks in others,” he said.

Tinker said not all populations are stagnant. The number of otters on remote San Nicolas Island, off Santa Barbara, has been growing dramatically, he said, despite a decision in 2012 to scrap a recovery plan there. The island population got as low as 12 animals in the 1990s, but it has since grown to about 70 otters.

High densities of otters can also still be found from Monterey to about Cambria, but Tinker said a growing shark population seems to be taking a toll. The biggest declines have occurred since 2005 between Morro Bay and Point Conception, he said.

Sharks are “the elephant in the room,” Tinker said. “The majority of carcasses are animals that were bitten by great white sharks.”

The southern sea otter is the smallest marine mammal in U.S. waters. The otters have voracious appetites and love to gobble sea urchins.

As many as 18,000 otters once roamed from Alaska’s Prince William Sound to Baja California, but they were killed by the thousands for their soft, thick pelts, which were considered a luxury starting in the late 1700s. The playful creatures were thought to be extinct in California by 1938, when a small population of about 50 was discovered near Big Sur. In 1977, they were listed as threatened under the Endangered Species Act.

How humans can help

Tinker said humans can help reduce otter mortality rates by controlling pollution and toxic runoff, which often flushes parasites, harmful algae and other toxins into the near shore habitats of otters. It is important, he said, because the animals are an important cog in the ecosystem, removing urchins that limit kelp forest coverage and crabs that kill important invertebrates in tidal creeks.

Despite all the obstacles, the population has been growing in fits and starts, with small declines in 2009 and 2010, which is what makes the lack of growth this year somewhat disturbing. The population counts would have to be at least 3,090 for three consecutive years before the California otter could be removed from the U.S. Endangered Species list.

“Sea otters are really important parts of the near shore marine ecosystem,” Tinker said. “The population overall is not decreasing, so the glass is half full, but there are some definite areas of concern.”

The Geological Survey count has been done every year since 1985 in early autumn and late spring along 375 miles of coastal waters from Half Moon Bay to Santa Barbara. The population numbers released each year are actually three-year averages of otter counts, which the Geological Survey recalculates annually.

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