A whale from the struggling population of endangered southern resident killer whales has died of massive trauma, but it is not known what caused the injuries to the three-year-old female.

The body of L112, known both as Sooke and Little Victoria as she was first spotted in January 2009 off the Victoria waterfront, washed up north of Long Beach, Washington, Saturday and a necropsy shows she died from "significant trauma."

The injuries do not show the usual characteristics of a boat strike, said Jessie Huggins, stranding co-ordinator with Cascadia Research, who conducted the necropsy with biologists and volunteers from other agencies.

"There was substantial trauma around the head, chest cavity and down the right side. It certainly caused the death, but we're not sure what caused the trauma," said Huggins, who is hoping a CT scan of the head and a raft of tissue tests will provide more information.

Tissue samples will be sent to U.S and Canadian agencies for contaminant, virology, bacteriological and biotoxin tests. Scientists will examine whether exposure to sonar had anything to do with the death, Huggins said.

"It's something the CT scans can sometimes pick up," she said.

A posting on the Cascadia website, giving details of the necropsy, said there were reports of sonar activity in Juan de Fuca Strait in the past 10 days and that members of K and L Pods were in the area at the time.

"We do not know if this whale was among those in the area, but the possibility is under consideration," it said.

Last week, the Canadian navy was criticized by environmental groups for using sonar in Juan de Fuca Strait, but the navy said all precautions were taken and no marine mammals were in the area.

The whale had been dead about three days when the body washed up, which means there was some decomposition, but overall body condition was good, Huggins said.

Processing of tissue samples could take several months, she said.

Whale researchers say the loss of a three-year-old female is devastating to the small population.

There is a 50 per cent chance of calves dying within the first year, but if they make it through the first 12 months, there is a good chance they will make it to adulthood.

"To lose a three-year-old is very sad, but especially when it's a female and especially from L-Pod is pretty devastating in a community this size," said Susan Berta of Orca Network.

Few females have been born to L-Pod in recent years.

The death drops the number of killer whales in the three pods to 88. There are also concerns about a calf born to J-Pod in December, which has not been seen in recent encounters.

Marine zoologist Anna Hall said it is sad to see a young animal die, especially because of the loss of breeding potential.

"Every single one of them is precious," she said.

It is possible the whale had underlying health issues before being struck or buffeted, Hall said.

"Killer whales are fast and manoeuvrable and, with a three-year-old, the family would have been nearby," Hall said.

"So what else was happening so the animal couldn't get out of the way?"

jlavoie@timescolonist.com