The woman was rescued from the water by emergency services and is being treated at the scene.
A Scottish ambulance spokesperson said that her condition was “critical.”
An air ambulance from Inverness landed on the nearby golf course and the woman was transfered from the harbour to the helicopter where she will be flown to Aberdeen Royal Infirmary.
A police spokewoman said: “Police were alerted shortly before 10am of a vehicle that had gone into the harbour at Macduff.
“Police are currently on the scene along with coastguard and fire and rescue. One woman was in the car and is being treated by medics.
“There will be a continued police presence while inquiries are carried out.”
Harbour Road in Macduff has now reopened after being shut for almost four hours.
Woman in “critical” condition after car plunges into north-east harbour