Waters achieved critical respect with his first screenplay, "Heathers" (1989), based in part on a fictional column he wrote while in high school. A cult classic, "Heathers" is a black comedy about high school life, depicting cliques, teen angst, suicide and murder sprightly directed by Michael Lehmann. Its success led Waters to work on two films for producer Joel Silver: "The Adventures of Ford Fairlane" (1990) and "Hudson Hawk" (1991). The former was a thriller about a detective trailing a mysterious woman who may or not be involved in the murder of a rock star; the latter was a tongue-in-cheek caper about a cat burglar coerced into stealing artifacts that, linked together, could transform lead into gold. Neither was a critical or box office success.

Waters fared better with his next original screenplay "Batman Returns" (1992). Continuing Tim Burton's dark interpretation of the comic strip, the realization of Waters' script received mixed reviews but his interpretation of the Catwoman character was singled out for praise. As embodied by Michelle Pfeiffer, she nearly stole the film and sparked the development of a separate spin-off feature (in development as of late 1995) that would reteam the star, director and screenwriter. Waters also contributed the witty script to the surprisingly watchable Sylvester Stallone sci-fi actioner "Demolition Man" (1993).