Aquatron is a side-scrolling shooter in which the player controls a spaceship over a planet completely covered with water. Unfortunately the planet is under attack and in each level, the player has to kill the steadily increasing opposition. The spaceship can be turned and is able to move both over and under water.

Ammo and shield (depleted after enemy hits) are limited, but can be replenished by collecting parachutes which are dropped by the home base (a zeppelin) which is stationed somewhere over the planet. One of the most important tasks is to keep it alive because the spawn points (an additional respectively new base appears) are far between - which means the player may have to survive without replenishment for a few levels when the base is destroyed. Enemies also drop parachutes which turn into submarines after reaching the water surface. The game has no defined end and is played for reaching a high-score.