Similar to Bust-A-Move/Puzzle Bobble, Bubble Heroes is an action-puzzle game in which the player shoots randomly colored bubbles at the other bubbles above. Once 3 or more bubbles of the same color are in contact, they pop and are removed from the screen.
There are 3 game modes: Story, Championship (both single-player) and Death Match (two players). The player must also pick a character before the start of the action proper, each with their own special power: a brave knight, a cat girl or a prince turned into a frog.
The Story mode tells you about the planet Radya and the four nymphs that need to be freed from the evil Gonzul. There are four worlds, each divided into two areas of five levels each. Most levels require the player to remove all the bubbles on screen without any of them reaching below a certain point, but some other level play a bit differently and require the player to free a nymph from the bubbles surrounding her. The last level of each world is played against a boss.
The Championship mode offers duels against all the characters from the game as AI opponents.
The Death Match mode let two players compete against each other, shown side by side on the screen.