The S.S. Linebeck can be customized and upgraded with various ship parts. These parts not only change the appearance of your ship but also provide defensive bonuses, making your ship more resilient to enemy attacks on the Great Sea. There are many different types of ship parts, categorized by material (e.g., Wood, Iron, Gold, Crystal). Each material offers different levels of defense. You can mix and match parts to create a unique look and optimize your ship's defense. Ship parts can be found in several ways:

- Treasure Chests: Many islands and hidden areas contain treasure chests with ship parts.
- Salvaging: Use the Salvage Arm to retrieve sunken treasure from sparkling spots on the sea. These often contain valuable ship parts.
- Mini-games: Some mini-games offer ship parts as rewards for achieving high scores.
- Trading: Certain characters on islands might trade ship parts for other items or Rupees.
- Defeating Enemies: Occasionally, defeated sea enemies might drop ship parts.
To equip ship parts, return to the S.S. Linebeck and interact with the ship's wheel. You'll enter a customization menu where you can swap out parts. Collecting a full set of matching parts (e.g., all Gold parts) often provides a significant defensive bonus. Experiment with different combinations to find what works best for your playstyle. Upgrading your ship is crucial for surviving the more challenging sea battles later in the game.