Atlantis is a first-person perspective puzzle game. The entire game is in 3-D. The HUD is basically a ‘window’ into the world of Atlantis, instead of moving a mouse around the screen, moving the mouse actually moves the screen itself. To interact with the world, the player must position the item, NPC or thing into the middle of the screen. Some critics have found this annoying, as there is no crosshair in the middle of the screen. This means the player must guess where the centre is, and move the screen accordingly. This has since been fixed in Beyond Atlantis and Beyond Atlantis II, where a crosshair is apparent.

Progression through the game involves solving various puzzles of varying difficulty. Some puzzles are extremely abstract and the solution is completely unexpected, whereas other puzzles are very simple. Another feature of Atlantis is having periods where the player must react quickly to certain events happening in the game. For example, in one section guards chase the player away from a certain area. If the player hesitates in moving backwards and looking for shelter, then the player will lose and will have to restart from the beginning of the scene. This can also be frustrating, as there is only one particular path the player may take, and taking any other part results in capture, death and restarting.

The Saturn version of the game supports the Saturn mouse, despite the fact that it was only released in Europe, whereas the Saturn mouse was only released in North America and Japan. European Saturns can be used with imported peripherals. The PlayStation version lacks the movement clips found in the other versions.