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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.
Squidward's Clarinet can be found in the game's files, but Squidward is never seen holding or using it.
Near the giant sand castle in Goo Lagoon is a sand sculpture of an Atari 2600 controller.
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.
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.
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.
According to some unused dialog in the game's files, Bubble Buddy was supposed to appear in Spongebob's dream.