In Deadly Duck the player controls the titular character who must shoot his bill bullets at crabs, the bricks they drop, and dragonflies.

Each level starts with eight crabs. The crabs grab bricks from the sides and try to drop them on the player-controlled duck. It is possible to shoot the crabs and the bricks as they fall, but if a brick lands on the duck, he dies. When a brick lands on an empty spot, it will stay on the pond for a moment, preventing the duck from moving horizontally.

On levels two to four there are two, four and six dragonflies, respectively, moving together just under the crabs. The player receives ten points for shooting the dragonflies, but this makes them angry. When angry, they drop one, two or three bombs (depending on the level). If the duck is next to a bomb when it explodes, he is killed. The game continues until the player runs out of ducks, which are equivalent to lives in other games.