Charles was born in Prince Rupert, British Columbia, Canada in 1962. He is the eldest of three children of Shirley Marie Menzies (née Naud), an elementary school teacher, and Harry Basil [Basso] Menzies, who is a commercial fisherman.
Charles spent his summers fishing with his father on the family's commercial fishing boat from the age of 12 until he was hired at the University of British Columbia in 1996. He earned the right to a full crew share seining salmon at the age of 15 and in the early 1980s earned the right to a full halibut crewshare. As a commercial fisherman Menzies fished halibut (longline), salmon (seine), and herring (seine) fisheries.
Charles graduated from Prince Rupert Secondary School in 1980. He subsequently completed an undergraduate degree in anthropology and sociology at Simon Fraser University in 1988. His graduate degrees in anthropology were completed at York University (MA in 1988) and City University of New York (PhD in 1998).