Although "Clu Clu Land" is the official English title for the game, "Clu Clu" is actually an anglicization of "Kuru Kuru"; a Japanese onomatopoeia that refers to something going "around and around". In order for Bubbles to move around the mazes, she must grab onto poles with her hands. When she holds on to a pole without letting go, she spins "around and around". The same phrase is also the basis for the title of the Game Boy Advance game Kuru Kuru Kururin.

In Clu Clu Land, the player is a female balloonfish named Bubbles, known as Gloopy[b] in Japan, who swims around in a maze trying to uncover all the golden Ingots.[13]

The story starts with a type of sea urchin, the Unira, stealing all of the treasures in the underwater kingdom of Clu Clu Land. Bubbles, the heroine, sets out to retrieve the treasure. The object of the game is to uncover all the gold ingots in each stage while avoiding the Unira and Black Holes. Ingots usually form a shape such as a heart or a mushroom. The only way Bubbles can turn around to change directions is by means of Turning Posts located throughout the stages. She can stun the Unira by using a Sound Wave. When they are stunned, she can push them into a wall to get rid of them and receive points. If Bubbles is hurt by the Unira, she will lose a life. A life is also lost if she falls into a Black Hole, or if time runs out. The game ends when Bubbles has lost all her lives.

In later levels, the player must pass over the ingots an odd number of times to uncover them, as they will alternate between their uncovered side and a dull side.