The game is viewed from a top-down, three-quarter perspective. Link explores islands, sails between them, enters dungeons, solves environmental puzzles, collects equipment, and defeats enemies to reach bosses.

The stylus controls movement and sword attacks, while acquired items add new ways to cross obstacles and interact with the environment. The overworld is traversed aboard the S.S. Linebeck, with charting, navigation, and sea encounters between island visits.

The Temple of the Ocean King is a recurring dungeon with a time limit represented by the Phantom Hourglass. Safe zones, shortcuts, and later equipment allow deeper progress on subsequent visits. A separate multiplayer battle mode lets two players compete locally using Link and phantom units.

Mark important locations, treasure spots, and unfinished paths directly on the sea charts. The maps can be annotated, and this is especially useful for remembering island clues and later item routes.

In the Temple of the Ocean King, plan each visit around the remaining sand in the Phantom Hourglass. Use safe zones to avoid time loss, activate shortcuts, and revisit earlier floors after obtaining items that open new routes.

Learn enemy patterns before committing to a sword strike. Keep fairies and potion supplies available for bosses, and use each dungeon item both in combat and on environmental targets, since many progression clues are built around its special function.