Mercury is a puzzle video game. The player can manipulate a droplet of mercury to move in the player's desire direction by tilting the stage using the PSP's analog stick. The player can use the directional buttons to toggle between focusing on all mercury droplets or a single droplet. The objective of each level in the game is to navigate the mercury around the stage and reach the goal. The HUD is made up of a time limit, a mercury level gauge, and a beacon count. To clear a level, all beacons on the level must be activated within that level's time and mercury limit. If the amount of Mercury on the level drops below the limit or time runs out, the level ends and must be restarted.
Each stage has hazards and obstacles designed to reduce the player's amount of mercury. The mercury can also be split into separate parts by using sharp objects or other hazards in the stage. Paint Shops are floating devices that change the color of the mercury once the mercury is under it. Some switches and doors only activate if interacting with mercury of a specific color. If the mercury is split up, the two droplets can be colored differently; if the two then merge, they form a new color. Color mixing is based on the RGB color model. For example, a red droplet and a green droplet can be merged to form a yellow one.
There is a total of six worlds. Each world is split into three Race levels, three Percentage levels, three Task levels, two Combo levels, and a final boss level. Race levels prioritize completing the level as fast as possible more than mercury count. Percentage levels emphasize preserving Mercury over quick completion. Task levels will have 1 to 6 beacons that must be activated to clear the level. Combo levels are either a combination of Race and Percentage levels or a combination of Percentage and Task levels. There are is each type of combo level in each world available before the boss. Boss levels are a combination of Race, Percentage, and Task. They are the last levels in each world and completing them will result in unlocking the next available world. If the highest score is achieved in all levels of one particular world, a bonus 13th level is unlocked. After all bonus levels are discovered for each world and also achieve the highest scores, a secret 7th world is unlocked.