Police say her seven-month-old son was taken to BC Children's Hospital where he remains in critical condition.
It's not yet clear how the mother and son came to be in the water.
Comox Valley RCMP S/Sgt. Ken Mazur said the police investigation indicates there was no third party involved in the incident.
Witnesses say they saw mother and child in the water near the Condensory Bridge around 2:30 p.m. PT. A number of them called 911.
A helicopter spotted the baby boy on one side of the river. He was picked up and airlifted to hospital around 3 p.m. PT.
About an hour later, the woman was found and pulled from the water, police said.
Comox Valley RCMP Const. Don Sinclair said a vehicle, which police believe was owned by the woman, was found near the bridge and helped police identify her.
"Our heartfelt sympathies go out to the family," said Sinclair, adding that the rescue was traumatic for all involved. He said some first responders may need counselling.