Aqua Bubble 2 is a color-matching game in which the player must shoot like-colored bubbles in order to remove these from the board and clear the level. Players must shoot a colored bubble onto a group of at least two bubbles of the same color, to create a group of at least three bubbles. When the bubbles are hit, these will pop and dissolve. The more bubbles are hit, the higher the points the player gets. Players must act quickly and determine which bubbles are worth shooting first in order to create the most number of bubble groups.
The game consists of several modes that have different objectives and degrees of difficulty. These are Recolor, Panic, Arcade, and Puzzle. In the Recolor and Arcade modes, the water level goes up only when all of the bubbles vanish. When the water container is completely filled, the player can move on to the succeeding level. In Puzzle and Panic modes, the water-meter level rises each time a bubble is shot. As it gets full, the bubbles descend one step. Players will not be able to advance to the next level until all of the bubbles on the gaming area are cleared. Players must be careful not to let bubbles touch the bottom of the game screen.