The undersea footage was shot in the Bahamas in the same location that was used for the silent 20.000 Meilen unter dem Meer (1916).
Cast members carried herring in their pockets to reward Esmerelda the sea lion after their scenes with her. Director Richard Fleischer was especially amused when the distinguished James Mason had to reach into his pocket after a shot. Fleischer said the cast smelled like the Fulton Fish Market.
Richard Fleischer was surprised at being considered for the director's chair for this film, as he was the son of Disney's biggest competitor, Max Fleischer. He approached Walt Disney to inquire if Disney knew who he was. Disney told him that he was well aware of who he was and hired him because he thought he was the best man for the job. Richard Fleischer also asked his father if he minded having his son working for his rival but Max Fleischer made no objection and even asked Richard to tell Disney that he thought he had made an excellent choice for his director!
Until the late 1960s, many of the sets representing the interior of the Nautilus were used as an attraction at Disneyland. This included the chart room, the salon, with organ, and one of the observation windows. The squid from the movie was fastened over the observation window and was animated so that the beak would emerge, snap several times, and then retract. When the building housing the "20,000 Leagues" display was needed for a newer attraction, the sets were removed and many were destroyed.