An unfinished dessert-themed area can be found in the game's files and was presumably going to serve as Patrick's dream in the 'Spongebob's Dream' level before it was changed to a dark room. It has no skybox and contains a couple of early concept models for Tikis and other objects.

According to some unused dialog in the game's files, Bubble Buddy was supposed to appear in Spongebob's dream.

Patrick has dialog for fighting Robot Patrick, King Jellyfish, the Flying Dutchman, and Robot plankton. Sandy has dialog for King Jellyfish, Robot Sandy, Prawn, Robot Spongebob and Robot Plankton. However, Patrick and Sandy never actually see or fight any of those bosses, making that dialog unheard in game.

During development of the game, there was a soccer ball that Patrick was to pick up and throw -- as seen in pre-release screenshots. In the final game, the soccer ball was replaced with a watermelon throw fruit.

Within the GameCube version, the folder for Goo Lagoon contains two folders, "New Folder" and "Working". These files hold early versions of Goo Lagoon. Trying to run them crashes the game, but opening the HOP files shows several early assets.

Near the giant sand castle in Goo Lagoon is a sand sculpture of an Atari 2600 controller.

Squidward's Clarinet can be found in the game's files, but Squidward is never seen holding or using it.

According to Chris Glass, a member of the game's development team, the texture used for the bark on tree trunks is simply a green-tinted photograph of feces.

Prawn, a villain introduced in SpongeBob SquarePants: Battle for Bikini Bottom, made a cameo in the SpongeBob SquarePants episode "Captain Pipsqueak", rehearsing lines with the rest of SpongeBob's rogues gallery. This is the first time a character from a SpongeBob video game has appeared in the series proper.

Inside the files of SpongeBob SquarePants: Battle for Bikini Bottom, you can find a video from Scooby-Doo! Night of 100 Frights, an earlier game by the same studio, Heavy Iron. It is unknown if this is a leftover from building Bikini Bottom off of 100 Frights' engine, or a cross-promotion that was veto'd by either Warner Bros. or Nickelodeon.

What some may find more interesting, however, is a now-deleted YouTube upload of the unused cutscene colloquially known as the "Cursed YouTube Video" which was based on a corrupted video file and as such featured disorientating, lagging sound; an inaccurate timer for video length; visuals that cut out; and a buffer that would begin at an exact point and continually play regardless of the viewer's internet speed.