His career began in the early days of silent film and culminated in two consecutive Academy Award nominations in the newly instituted (but short-lived) category of Best Assistant Director.

Only a few of his assistant director credits from the 1910s have been recorded, with vehicles for Carlyle Blackwell (The Shadow of a Doubt, 1916) and Harold Lockwood (The Avenging Trail, 1917) listed among the earliest titles.

[2] At this point, as the talkie revolution transformed Hollywood, Waters, now an MGM contractee, returned to his former profession as assistant director, an industry job title which, during a brief period covering five Academy Award cycles (1932–33 to 1937), became eligible for an Oscar.

Only John Waters, among the previous year's eighteen nominees, was renominated, as his contribution to Wallace Beery's portrayal of Mexican revolutionary leader Pancho Villa won against two Claudette Colbert–Warren William titles represented by assistant directors Scott Beal (Imitation of Life) and Cullen Tate (Cleopatra).

Other than a 1935 one-reel Pete Smith Specialty, Donkey Baseball, his sole directorial assignment in the sound era was The Mighty McGurk, MGM's 1946 vehicle for his old Viva Villa!