Stonkers is controlled either using keyboard or joystick. In the game, the player controls infantry, artillery, tank, and supply-truck units. Combat units consume supplies over time and the player must use the supply units to replenish them. Supply units are unloaded while a ship docks at the player's port. Information about ongoing events is displayed in a ticker tape on the bottom of the screen.

Stonkers is controlled either using keyboard or joystick. In the game, the player controls infantry, artillery, tank, and supply-truck units. Combat units consume supplies over time and the player must use the supply units to replenish them. Supply units are unloaded while a ship docks at the player's port. Information about ongoing events is displayed in a ticker tape on the bottom of the screen.