The body of the 18-year-old orca, identified as J-32, was spotted floating Thursday near Courtenay and Comox on the east side of Vancouver Island.
Paul Cottrell, the Pacific marine mammal co-ordinator with the Department of Fisheries and Oceans, said the death of the sexually mature female will be felt by the pod.
"It's a huge loss," he said Friday from Comox. "There aren't that many breeding females and especially a young one that would have contributed for decades."
J-32 was from the so-called southern resident pods that ply the waters off British Columbia and Washington state.
Canada and the United States have declared the whales endangered, and their critical habitat has been identified on both sides of the border in the Salish Sea, Juan de Fuca Strait and Puget Sound.
Female orcas reach maturity at about age 15 and usually have a calf every three to five years until they reach 40 to 45 years old.
Cottrell said there were no obvious signs of death on the animal. It likely died in the last few days, he said.
A team of experts from the Fisheries Department, the Vancouver Aquarium and the B.C. Animal Health Centre will participate in a necropsy on the animal this weekend.
Dr. Peter Ross, the director of the aquarium's Ocean Pollution Research Program, said the loss is tough for recovery efforts of the whales.
"This is profoundly disappointing for a very small population of killer whales that we've been watching, that everyone has been watching, for which there exists a lot of conservation concerns."
Ross said a calf was born last September within the southern residents, but it died a few months later. It's been a few years since the last calf was born, he added.
Ross said there is plenty of hope for the iconic orcas that thousands of people pay to watch on tour boats off B.C. and Washington every year.
"Even small populations of killer whales can thrive and they do so almost despite the odds out there in the natural world."
The whales are smart, they socialize, they teach and they learn to adapt, he said.
"These are animals that have probably evolved an ability to survive, maybe not prosper at this juncture, but certainly survive in evolutionary terms. And they probably do so in the face of what would be potentially adverse numbers."
Often when a killer whale dies it simply disappears into the ocean. Cottrell said researchers were very lucky that someone was able to spot J-32 and call the B.C. Marine Mammal Response Network.
"This only happened because it was called in and we were able to secure the animal," he said. "So we're going to get some useful information from this animal."