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.