Bubble Game 3D is a bubble-popping game that features unique three-dimensional graphics. It presents the classic purple playfield in a tabletop format from an angled, top-down perspective. The player's goals are to clear the field and earn points by shooting bubble projectiles at rows of mixed-colored bubbles. They earn the most points when they drop avalanches of bubbles and earn consecutive combo multipliers.
The player pops clusters of three or more identical bubbles. They receive an arrow shooter near the bottom-center of the table with a projectile at the base. Unlike the rest of the game, the white arrow looks flat and two-dimensional. That said, the player can stretch it in any side-to-side or upward direction to make each shot more targeted and precise. When they shoot a cluster with non-matching bubbles beneath it, they create a powerful points-earning avalanche that drops off the screen. If they pop bubbles in a streak, they multiply the points they receive in the upper-right corner.
Bubble Game 3D supplies five gray penalty pass bubbles to the left of the shooter that allow the player to fail to create clusters five times. Before the penalty, it attempts to distract them by making bubble colors dull and flash at random. Afterward, they receive a penalty of one or more rows dropping onto the field. Each time, they receive fewer opportunities to fail because the reset for the passes decreases by one. The game offsets this issue by resetting the passes to five after the player receives five penalties.