The gameplay is largely the same as the original version of The Wind Waker on the GameCube; however, the game offers graphical modifications and various new features not included in the original. The Wii U GamePad's touchscreen serves as a map and inventory, eliminating the need to toggle between gameplay and the menu interface. Players can use motion controls to control the Wind Waker.[9] Some equipment, like the bow, can be aimed using the GamePad's gyroscope, as in Ocarina of Time 3D. The game offers Off-TV Play which enables the player to play the game solely on the Wii U GamePad. The game can also be played on the Wii U Pro Controller, a controller similar to the one used in the original game.[10]

The Tingle Tuner item, which The Wind Waker utilizes via the Game Boy Advance as a peripheral to the GameCube, has been replaced with an item called the Tingle Bottle. The Tingle Bottle is used to send messages to the game's Miiverse community if players are in need of help; players then receive replies containing hints as to current objectives. Using the Picto Box item in the game, players are able to take screenshots, including self-portraits, switching between happy, sad, and surprised facial expressions for Link. They can then post these screenshots to Miiverse for other players to see