Players can play "The Rise of Atlantis" by solving tile puzzles that involves matching up similar symbols in a vertical or horizontal line. Once three or more tiles are aligned, the symbols are removed from the board. A round ends when Poseidon's artifact become completely visible.
Each stage in "The Rise of Atlantis" is designed so that the final piece of the Poseidon's artifact puzzle is found when the pieces are cleared from the last remaining row. The aim of "The Rise of Atlantis" is not to make as many symbol matches as possible, but to ensure that all of the artifact pieces are freed from the game map. Each round also features a timer that results in a life loss for the player every time it reaches an empty bar.
"The Rise of Atlantis" also features various in-game power-ups that are designed to help the player clear tiles at a faster rate. These power-up tiles include the Bomb, Lightning and Sun tiles. When used, the Sun tile clears several tiles that are randomly chosen. This power-up is refilled every time the player matches four or more tiles. The Bomb tile is used to clear tiles from a selection section. The Lightning tile is used to clear tiles that have the same symbol design.