Treasures of the Mystic Sea is a timed, pirate-themed match-3 game. The player's goal is to remove all hexagon-shaped wood tiles, also referred to as chips, from a playfield of hanging blue hexagon-shaped spaces filled with objects related to a pirate's life (i.e., curved cutlasses, flintlock pistols, locked chests, navigation compasses, one-eyed skulls, rum bottles, treasure maps, white dice and wooden barrels). When they win, they receive points and achievement awards for performing specific tasks, such as creating long lines and removing a specific number of the same type of object.
The player can only break the wood chips by removing lines of three or more identical objects on top of the pieces. They must break all chips before the water in a blue vertical gauge timer on the left side of the screen runs out. The hexagons create a beehive layout that only permits horizontal and diagonal alignments instead of vertical ones. When the player completes a line, a cascade of new objects flows down the screen into the spaces revealed when the objects and chips disappear.
Treasures of the Mystic Sea also gives the player six automatic boosters whenever they align an object with a glowing color around it. These boosters perform swaps and removals. A booster might suddenly swap random chips or two of the same type. It might also remove random chips, horizontal lines, circular areas or specific types.
These boosters are especially helpful as the player proceeds across the map. New locations offer up exciting and difficult challenges, such as chains and locked shackles that the player must first unlock before they can perform alignments.