A coalition of dentists, doctors and professors campaigned to keep fluoride in the water, but councillor Murry Krause said in the end democracy won out.
"I know the dental community will be disappointed and I think some in the medical community will be disappointed, but we put it to a fair vote and I'll be supporting it," said Krause.
In the referendum, which was held during the Nov. 15 civic election, 10,171 people voted to end fluoridation while 8,764 voted to keep it.
Prince George has been fluoridating its water since 1955.
Two other B.C. communities also held votes on the issue. In the city of Cranbrook people voted to keep it. In Sparwood, people decided to scrap it.
There are only three other communities in B.C. that fluoridate water: Fort St. John, Prince Rupert and Terrace.