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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.
The undersea footage was shot in the Bahamas in the same location that was used for the silent 20,000 Leagues Under the Sea (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.
After the Nautilus rams a ship and we see how it sinks down through the water, some of the bubble-streams are animated to hide the wires that support the ship-model.
The climactic squid battle on the Nautilus was originally shot with a serene sunset and a calm sea. Director Richard Fleischer was troubled by the look of it because the cams and gears that operated the squid could easily be seen, making it look obviously fake. Walt Disney visited the set one day and Fleischer told him about the problem. Disney came up with the idea of having the squid battle take place during a fierce storm (another story is that it was actually screenwriter Earl Felton who came up with the idea). The scene was reshot that way and is considered by many to be the highlight of the film.