By John Boxley, Producer, NBC News

SAN PEDRO, Calif. -- Along Southern California's pristine coastline, ailing sea lions are turning up in record numbers.

"We have a lot of little pups this year," said veterinarian Lauren Palmer, who is nursing them back to health. Most are about eight months old, she said, and appear dehydrated and malnourished, having trouble adjusting to life away from mom. For some reason many pups are leaving their mothers early. It's not clear why.

Usually, around this time of year, there might be a dozen sick sea lions in San Pedro, said David Bard, operations director for the San Pedro Marine Mammal Care Center. But so far, the care center has taken in nearly 200 and counting. Last week alone, there were 50 new cases.

"It’s a pretty big spike,” he said.

The last big spike was in 2009 when the care center took more than 500 sick animals, but most of those were elephant seals. Researchers say that was due to El Nino conditions.

Looking for answers
During a tour of the facility, Bard pointed to a group of new arrivals.

"You can see the activity level of these fellows is a little low, they don’t have as much energy," he said. There were about 20 pups inside a small pen area, each looked quite lethargic.

So, what’s happening to the sea lions this year? So far nobody knows. There are plenty of theories, however, such as food shortages, climate change or simply an increase in the number of sea lion births.

"We are not seeing a disease outbreak among these animals or any obvious underlying cause," Bard said.

So, researchers continue to collect data and blood samples from the sea lions, looking for answers.

"We are very, very busy," said Palmer.

When asked if she feels overwhelmed, she laughed and replied, “Some days, yes."

And San Pedro is not alone. Last week, the Pacific Marine Mammal Center in Laguna Beach declared their organization in a “state of emergency” as it continues to see an onslaught of California sea lion pups in need of medical attention.  

“We are seriously concerned about the pace at which animals are stranding, and having the resources to keep up," said Michele Hunter, director of animal care.

Pups recover with treatment
Bard, in San Pedro, says caring for so many sick animals has not only been taxing for staff and volunteers but also to the bottom line at their non-profit. But he said the Marine Mammal Care Center is committed to treating each case and responding to all the challenges, while "staying optimistic."

The biggest challenge right now, he says, is managing the dwindling budget. The animals are here for about two months at a cost of nearly $2,000 per sea lion.

There is some good news: most of the sea lions are responding to treatment, which begins with a liquid diet and fish smoothies. Later the pups are fed herring. Palmer says it's a great feeling knowing that they are making a difference and giving these animals a second chance.

Bard admits that watching them leave is hard.

"We put a lot of hard work and effort in treating them successfully, we take them down to the beach and then we see them go, probably forever,” he said. “It’s a rewarding feeling, most rewarding job I have ever held, but at the same time, it’s a little bit bittersweet."

Army Corps of Engineers

A sea lion feasts on a salmon along the Columbia River.

Two Pacific Northwest sea lions found shot dead this week, along with at least 18 others in the last two months, make up what one expert calls an "unprecedented" attack on marine mammals protected by federal law.

For years, sea lions along the Columbia River between Oregon and Washington have been gorging on salmon, and experts suspect angry fishermen have retaliated by killing some.

"Unfortunately and not unexpectedly, these deaths coincide with the spring run of salmon," Robin Lindsey, a member of the Seal Sitters Marine Mammal Stranding Network, told msnbc.com.

A few killings are typically seen at the start of each season along the Columbia River, but this year is running about four times the norm, Dalin D'Allesandro, a Portland State University research assistant, told The Oregonian. 

"Since the beginning of April, we've seen a surge in both Steller and California sea lions being shot," said D'Allesandro, who helps the local marine mammal stranding network.

The increase also comes after federal officials in March authorized local authorities to cull up to 92 California sea lions a year in waters just below the Columbia River's Bonneville Dam. Biologists estimate sea lions have eaten between 1.5 and 4 percent of returning salmon.

Related: 8 sea lions found shot to death near Seattle

Jim Rice, coordinator for the Oregon Marine Mammal Stranding Network, is among those who suspect that was also a factor in the dramatic increase.

It "may encourage some people to shoot sea lions" thinking they've got a green light as well, he told msnbc.com.

"Marine mammals have been protected since the early '70s," Rice earlier told The Oregonian. "Prior to that there were actually bounties on the animals and they were hunted quite actively. It is certainly unprecedented within that time frame."

As for the number of sea lions killed in recent months, Rice says the number is probably more than the 20 reported. "There are likely others that never came ashore or have not yet been reported to stranding network responders," he noted.

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Richard Clement / Reuters, file

Sea lions rest inside an open cage on the Columbia River at the Bonneville Dam in North Bonneville, Wash., in April 2008.

Oregon state authorities can resume killing California sea lions that feast on endangered salmon bottled up at a dam on the Columbia River, but fewer than one-third as many as federal biologists previously had authorized, a judge has ruled.

U.S. District Judge James E. Boasberg in Washington, D.C., on Thursday denied the Humane Society of the United States' request to stop the killing at the Bonneville Dam while a lawsuit challenging the program goes forward. But he limited the killing to 30 animals a year instead of the 92 authorized by federal authorities, and ordered that none of them may be shot. 

"Obviously we are very disappointed that this program was not halted," said Sharon Young, marine issues field director of the Humane Society. "But, we are grateful that the court put some restraints on it."

It was the group's third attempt to permanently halt the killings since they started in 2008.

The floating traps are out and if any of the 92 California sea lions branded as regular salmon eaters are seen inside them, the gates will be sprung, and the animals killed by lethal injection, said Oregon Department of Fish and Wildlife spokeswoman Jessica Sall. She said they have no plans to shoot any animals. California sea lions that hang around the dams eating salmon, and refuse to leave despite hazing by rubber bullets and firecrackers, go on a kill list.

Adult salmon and steelhead returning to spawn get bottled up at the fish ladders over Bonneville, located east of Portland, Ore. California sea lions, which are federally protected as marine mammals, but not as threatened or endangered species, swim about 145 miles upriver to the dam to feed on the fish in the spring.

Since 2008, 28 sea lions have been killed and 10 placed in institutions under similar salmon-protection programs overseen by the Fisheries Service.

The limits imposed by the judge should not pose a problem, Sall said. The department did not anticipate killing more than 30 animals in any one year. Over the past four years, only 41 have been trapped and killed or sent to a zoo or aquarium. The current authorization from the National Oceanic and Atmospheric Administration's Fisheries Service is good for four years.

The Humane Society lawsuit contends that the Fisheries Service erred when it decided that sea lions eating up to 4.2 percent of the fish passing over the dam amounted to a significant obstacle to the restoration of endangered salmon, when fishermen are allowed to take up to 17 percent. It adds that killing sea lions will have no effect on restoring salmon, which face a greater threat from fishermen and predation by walleye and bass introduced into the river for sport fishermen to catch.

The department, a co-defendant in the case, counters that while sea lions kill some protected salmon, fishermen are only allowed to kill hatchery-bred fish. The department says it is able to estimate how many wild fish die after being released, and to shut down the season if necessary.

Salmon returns to the Columbia Basin in Oregon, Washington, Idaho and Montana have declined steadily from harm caused by dams, logging, agriculture and urban development since settlement of the region began in the 1840s. Only a small percentage of the fish are wild, with the great majority produced in hatcheries. There are 14 different types of wild salmon and steelhead in the Columbia Basin protected by the Endangered Species Act.

The Associated Press and Reuters contributed to this report.

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Elaine Thompson / AP

This dead sea lion with bullet wounds was found on a West Seattle beach on Jan. 23.

A group best known for fighting off whalers has joined federal investigators looking into the recent killings of sea lions near Seattle, offering a $10,000 reward for information leading to the arrest and conviction of whoever is responsible.

Another sea lion was found dead over the weekend, adding to seven others found in recent weeks with bullet wounds. A harbor seal was also found dead.

Federal officials planned to examine the latest sea lion on Tuesday to determine if it, too, had been shot. 

The latest sea lion found was on the Nisqually River, south of Seattle, as were six of the other sea lions.

Robin Lindsey / sealsitters.org

Officials examine a dead sea lion found on a Seattle park beach on Jan. 23.

"This is a violation of U.S. federal law and the person or persons responsible for these shootings must be apprehended and brought to justice," Paul Watson, founder of the Sea Shepherd Conservation Society, said in announcing the reward late Monday.

Watson, who is on a Sea Shepherd ship off Antarctica pursing Japanese whaling ships, noted that his group has offered rewards in the past, including one that led to the arrest of a man convicted of killing 22 seals in New Zealand.

STORY: 8 sea lions found dead

The suspicion has been that sea lions in the Seattle area's Puget Sound are being targeted because they devour salmon, thus reducing what's available for fishermen.

"Sadly, shootings occur annually in the Pacific Northest, particularly in fall and winter when large numbers of sea lions move into our area in search of food," Seal Sitters, a group that responds to marine mammal strandings in the Seattle area, noted in its blog. 

Sea lions are certainly feeding this winter, including the Nisqually, where a state wildlife biologist recently took photos of a large congregation. "This is the most sea lions I have ever seen at once in south sound," Pete Topping told the Seattle Times of the Dec. 24 sighting.

Chris Phinney

Dozens of sea lions were spotted on Dec. 24, 2011, on an anchored barge in the Nisqually Delta by Pete Topping, a Washington state wildlife biologist.

Firecrackers and even rubber bullets have been used by officials to try to scare off sea lions but to little avail. Some known to be California sea lions that migrated north have been captured and trucked back. Those that end up returning and are spotted are killed.

Anyone with information was urged to contact the federal investigation hotline at 800-853-1964. "The information can be provided in confidence and the source can remain confidential," Sea Shepherd said in a statement.

Penalties could range from fines to jail time. One of the animals killed was a Stellar sea lion, a species protected under the federal Endangered Species Act.

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