Waters was privately educated at the Calvert School in Baltimore. High School in Towson, Maryland, and Calvert Hall College High School in nearby Towson, he graduated from Boys' Latin School of Maryland. While still a teen, he made frequent trips into downtown Baltimore to visit Martick's, a beatnik bar, where he and Milstead met many of their later film collaborators. He was underage and couldn't enter the bar proper, but loitered in the adjacent alley, where he relied on the kindness of patrons to slip him drinks.
MGM's The Wizard of Oz (1939) had a profound effect on Waters' creative mind, He said about it: Waters's first short film was Hag in a Black Leather Jacket.