The three goddess statues are actually a reference to Pikmin. The Din statue has a nose like a Red Pikmin, The Faore statue has ears like a Yellow Pikmin, and the Nayru statue has a crack that looks like a mouth, the defining trait of a Blue Pikmin.

Link's body has animations for swimming and floating idly, but as all of the water in the game is opaque, the animations are never seen in the game. The only way to see them is by going into the game's unused test rooms, as they have clear water.

Koboli, the postman found behind the counter found on Dragon Roost Island, was designed after the Postman from Majora's Mask. Through Zelda lore it is believed that the Running Man from Ocarina of Time is one of Koboli's ancestors, since the Zelda timeline makes it impossible for the Postman and Koboli to be related.

In the E3 2002 trailer, the song "Riddles of Steel" from the 1982 film Conan the Barbarian is used. This song was also used in the commercial for Ocarina of Time, and was later used in the E3 2004 trailer for Twilight Princess.

Link is voiced by Sachi Matsumoto, the same actor who voiced the Skull Kid from The Legend of Zelda: Majora's Mask.

Since Link is left-handed in this iteration, he holds the Wind Waker in his left hand, while a conductor would more properly hold the baton in their right hand. Despite this he still uses the baton to adjust what time to play in, and his free hand to signal the pitch, just as a conductor would do, but with the opposite hands.

In the Italian release of the game, Tetra is named "Dazel", which is an anagram of "Zelda."

After development of the first game, Nintendo was considering developing a sequel with the working title 'Wind Waker 2'. According to producer Eiji Aonuma, the demand for a more Ocarina like game with Zelda made them reconsider the idea. Artist Satoru Takizawa stated The game would've been set on land rather than at sea.

"To tell you the truth, we had begun the initial steps towards creating Wind Waker 2 around that time. However, demand for a more Ocarina-like game was growing by the day. We did our very best with Wind Waker, and put everything we had into it…
However, Wind Waker 2 would have taken place in a more land-based setting, rather than on the sea, so that we could have Link gallop across the land on a horse.

But Link’s proportions in Wind Waker weren’t very well suited for riding on horseback, he was too short, and an adult version of Toon Link did not seem appropriate either. So, while we were stuck on those problems, we became aware of the greater demand for a more realistic, taller Link. High-budget live-action fantasy movies were also huge at the time, so with all things considered, we decided to have at it. I was on board with the project as art director, and started off by bringing [Yusuke] Nakano on to do the design for Link."

In 2016, an American livestreamer discovered that the boss of the Forbidden Woods, Kalle Demos, could be killed in one hit by pouring a bottle of the Forest Water (found in the Forest Haven) onto its exposed flower head, after a user in her chat jokingly suggested using the Forest Water to water the plant monster. While this trick was performed while playing the Wii U remaster, NintendoLife tested and confirmed that this secret exists in the original GameCube release.

The Master Sword being a sword that would get pulled out from its pedestal by those chosen appears to be derived from the Arthurian Legend of Excalibur, also known as the "sword in the stone". Similar to how King Arthur was divinely chosen to be able to pull out Excalibur, Link was given the power by the Goddesses to pull out the Master Sword. Because of these similarities, the Master Sword was renamed to "Excalibur" in the French localizations of The Legend of Zelda: A Link to the Past, The Legend of Zelda: The Wind Waker, and The Legend of Zelda: Twilight Princess.

Link can use the Grappling Hook to steal various items from enemies, but there are only two which will have a cosmetic change when an item is stolen: the Darknut with his Knight's Crest, and the Moblin with his Skull Necklace.