PixelJunk Shooter is a shooting game where you fly a subterranean vehicle to rescue scientists trapped underground. You control movement with one stick and shooting with the other. This combines with the world's physics to create a puzzling shooting challenge.

Play involves flying your craft and using missiles to defeat enemies and destroy weak rocks. You can manipulated three types of fluid you find (water, magma, and ferrofluid) to reach the survivors. This adds a puzzle aspect to the action, and uses physics to simulate the materials. Shoot out rocks to release some water down onto lava and you create solid rock.

These physics extend to how your craft moves. You turn left and right and fire a propulsion jet with the left stick. With these simple controls you need to carefully stay afloat and negotiate complex caverns. While you do this the right stick controls your rockets and grapple hook.

To progress to the next area you need to rescue a certain number of scientists. As you do there is a narrative about how the scientists became stuck and wider plans afoot.