Chief Fire Officer Jamie Ramsay said the crash was reported to emergency services at 12.10pm and crews from Lookout Point and Portobello attended.
Two people were believed to be inside the vehicle at the time of incident, and had to swim to shore, CFO Ramsay said.
Qualified Firefighter Liam McCall, who attended the scene, was seen attempting to remove about 10 paint cans which had spilt inside the vehicle.
"A driver has ended up in the harbour, and you can see a bit of house paint has started to spill from the vehicle, so we have Mr McCall in painter overalls trying to reduce the pollution," CFO Ramsay said.
A St John spokeswoman said one ambulance had attended and taken one patient with moderate injuries to Dunedin Hospital.
Local resident and community board member Hoani Langsbury was at the site and said he had been alerted by an ongoing car horn.
"I thought there was a kid in a car because I heard the horn going off," he said.
He had brought blankets for the victims from his home when he discovered they were "soaking and covered in paint".
A police spokesman said a tow truck had been sent to assist in the removal of the car from the harbour.
