I can't figure out how to get the Spirital stone of water. I have been stuck on this for a while!
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Follow the river outside Hyrule Castle (Zora River) until you reach a waterfall. Play Zelda's Lullaby and jump through to Zora's Domain.
Talk to King Zora, then go play the Zora mini-game where you dive into the water from high up. The prize is the Silver Scale. Use this to dive through the hole under the water to reach Lake Hylia.
Dive for the bottle under the water nearby. Open it up and read it. Show it to King Zora and he'll let you through. Put a small fish into your bottle and drop it in front of Lord Jabu-Jabu.
Find Princess Ruto in the dungeon, get the Boomerang so that you can destroy the tentacles in the rooms, use the Princess to weigh down switches, find the Spiritual Stone and throw the Princess to it, defeat the mini-boss, defeat the boss, and there you go.
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