The game is divided in five worlds (listed as "chapters"): Bikini Bottom, The Center of the Earth (an underwater volcano), Prehistoric Bikini Bottom, Rock Bottom, and Industrial (the industrial district of Bikini Bottom). Each world is divided into four levels, which are cleared by collecting the object desired by Barnacle Boy. In addition, the fourth level of every chapter has a boss enemy who must be defeated to progress.
Scattered through all the levels there are spatulas. By collecting all 100 in a level, SpongeBob earns an extra life. In the PlayStation version, spatulas serve as Sonic the Hedgehog-style health measures for the player. If SpongeBob is touched by an enemy, he loses all of the collected spatulas, and if he is touched by an enemy without any spatulas, he loses a life. In the PlayStation version, there is a continue feature that features Patrick at SpongeBob's house all alone; he encourages the player to keep going on SpongeBob's quest by saying where are his friends, and thinking they forgot his birthday. In the Game Boy Advance version, a separate health measure is used, which can be replenished by collecting items like Salty Fries, Salty Shakes, and Krabby Patties. Lives also can be obtained by finding underpants.
In the PlayStation version, by collecting a certain number of spatulas in every chapter, a secret level named "Six Clams Adventure Land" (a reference to the Six Flags amusement park) can be unlocked. In those levels, set in an amusement park, SpongeBob must ride through obstacles and collect all 25 flower tokens. These tokens can be used to buy props for Patrick's birthday party at the end of the game.