Comox Valley RCMP say the woman was pronounced dead at hospital just before 7 p.m. Friday, after being pulled from the chilly Puntledge River hours earlier.
Her seven-month-old son has been airlifted to B.C. Children's Hospital in Vancouver, where he remains in critical condition.
"Our heartfelt sympathies go out to this family," said Sgt. Kevin Mazur in a statement issued Saturday.
"Based on the evidence and information we have gathered so far, there is no indication that any third party was involved in the pair entering the water," Mazur said.
Mounties say two passersby called police at about 2:30 p.m. after seeing the pair floating in the fast-flowing river near Lewis Park and the Condensory Bridge in Courtenay. It is not yet clear how long they had been in the water.
Officers arrived within minutes and deployed a boat and a helicopter. Comox Valley search and rescue had two or three boats in the water, and Courtenay Fire also responded, said RCMP Const. Don Sinclair.
"It was a very big undertaking, a great response by all of our emergency crews in the area," he said by phone on Saturday.
He said helicopter crews first spotted the baby and he was rescued just before 3 p.m. and taken to hospital. But the mother had disappeared under the churning waters, and she was not pulled out until 4:12 p.m.
The massive rescue effort drew a large crowd of bystanders, with more than 50 people watching the search unfold, said Sinclair.
Once the woman was found, she was rushed to St. Joseph's General Hospital in Courtenay. Despite the efforts of multiple medical workers, she was pronounced dead at 6:55 p.m.
There is still no indication of how the pair wound up in the water, but a vehicle has been found parked near the Condensory Bridge that officers believe belongs to the woman, said Sinclair.
He said the mother and son have been identified and next-of-kin have been notified, but their names are not being released at this time.
The B.C. Coroners Service has now taken the lead in the investigation, with ongoing assistance from the Comox Valley RCMP.
Investigators are asking anyone who may have seen the pair near or in the water before 2:40 p.m. on Friday to come forward. Sinclair said on Saturday afternoon that no one had contacted the detachment yet, to his knowledge.
He said the Puntledge River is a mountain-fed river, so the water on Friday was frigid. He reminded Comox Valley residents to practice water safety.
"Stay away from the river. It's moving extremely fast and it's very cold," he said.
— By Laura Kane in Vancouver