Officials say the first calls came in reporting a boat listing to one side and travelling erratically at about 3 p.m. PT.
By the time rescue crews and a helicopter from CFB Comox arrived, the boat had run aground onto the rocky shore.
Police say they pulled a man and a woman from the water.
The 44-year-old man was taken to hospital and later released. The woman was pronounced dead at the hospital.
Comox Valley RCMP and the B.C. Coroners Service are investigating.