The player plays as SpongeBob, Mrs. Puff, Lincoln Loud, Michaelangelo (Michaelangelo, Lincoln Loud, Babe Carano, and Mrs. Puff must be unlocked) and try to get to the end of difficult driving courses without the characters boat overturning. If the player successfully beats a driving course, they unlock a character and their boat parts. The driver and boat can be mixed and matched but it has no effect on gameplay. After the player beats all the courses they unlock a final course. When the final course is beaten, the player wins the game.
Unlike the first two Boat-O-Cross games, this game is a crossover with other Nickelodeon shows.