The Great Fairy of Power had told Link to visit a friend of hers by Hyrule Castle, so Link found a small passageway that led to another Great Fairy's fountain. This fairy, the Great Fairy of Magic, gave him Din's Fire, a spell that could be used to attack and burn things.

Link didn't know where to go next, so he played Saria's Song to talk to Saria telepathically. The Deku Tree had once told Saria that King Zora, ruler of Zora's Domain, had the last stone, the Spiritual Stone of Water. Link had scant knowledge of Hyrule's geography, so acting on a hunch he left Hyrule Castle Town and began following Zora's River up to its source. Before long he met the owl again, who told him:

Just ahead lies Zora's Domain. The Zoras serve Hyrule's Royal Family by protecting this water source. Their door will not open for anyone except those who have some connection with the Royal Family. Let them hear the melody of the Royal Family!

Link followed Zora's River until he reached a large waterfall. Link read a stone tablet set into an overhang in front of the waterfall:

Sleepless Waterfall
The flow of this waterfall serves
the King of Hyrule. When the King
slumbers, so too do these falls.

Playing Zelda's Lullaby on his ocarina, Link watched as the waterfall's flow lessened, and a door behind the falls was opened. He jumped through the waterfall and entered Zora's Domain, home of the proud aquatic people, the Zoras. Talking to the Zoras, Link discovered some important things: their Princess Ruto was missing, and Zoras had searched as far as Lake Hylia for her; Lord Jabu-Jabu, the patron deity of the Zoras, lived in Zora's Fountain; Ruto had been in charge of preparing Jabu-Jabu's meals; one could enter Zora's Fountain only with King Zora's permission; and, according to the "Legend of Zora," the act of offering a fish to Lord Jabu-Jabu would make one happy.

Link won a silver scale in a diving game, which allowed him to breathe underwater longer. He used the silver scale to enter a warp portal that led to Lake Hylia, where it was rumored that the river carried many things. At the bottom of the lake Link found a bottle with a note in it, and he carried it straight to King Zora. The King expressed dibelief that Princess Ruto had been swallowed by their guardian deity Jabu-Jabu, as the note said. He realized that Jabu-Jabu had been "green around the gills" ever since the evil Gerudo thief had come around. King Zora implored Link to rescue his daughter, and moved aside to let Link into Zora's Fountain.

Link had caught a fish in a bottle, and recalling the "Legend of Zora," offered the oversized Jabu-Jabu his little fish. Jabu-Jabu opened his mouth and sucked in, swallowing both the offering and and the offerer. Inside Jabu-Jabu's belly, Link dodged Biri and Bari, electrified flying jellyfish, and discovered that parasitic tentacles and many other vile creatures had infested Jabu-Jabu.

Link finally found Princess Ruto, but she was not happy about being "rescued." She had been going inside Jabu-Jabu ever since she was little, only this time he had swallowed her by accident and she had dropped her precious stone. Link had to carry her around as they looked for the stone, because she wouldn't leave without it.

They found the Zora's Sapphire, but it was a trap: Ruto was kidnapped and Link did battle with Bigocto, a huge slimy Octorok. Delving deeper into Jabu-Jabu's belly, Link found a giant monster studded with protective Biri: the bio-electrical anemone Barinade. Link brought down the creature's defenses, dodging electricity and whirling Biris, and saved Princess Ruto.

After they had warped out safely, Ruto finally admitted that Link was cooler than she had thought, and gave him the Zora's Sapphire, the Spiritual Stone of Water, after he promised not to tell her father. Her mother had told her to give the Stone only to the man she was going to marry, so the stone was her most precious possession.

Swimming out, Link noticed a patch of dry land. He swam over to it and noticed that the cliff side was fragile. He planted a bomb and blew a hole in its side. Inside, Link met the Great Fairy of Magic, who gave him Farore's Wind, a warp spell.