Ok I'm not sure if I already asked this or not but how do you get the third..

Zora's Sapphire is used to open the path in the Temple of Time. The silver and gold scales are used to dive deep in the water, and questions on how to get the scales are answered below.

To get the last spiritual stone, go to the Zora River, near the entrance to Kakariko Village, and blow up the boulders with bombs, make your way up, and play Zelda's Lullaby to part the waterfall.
To get past King Zora, show him the bottle with Princess Ruto's message inside it (obtained by having the Silver Scale and diving for it at Lake Hylia). To get inside Lord Jabu-Jabu's Belly, drop a Fish in a bottle in front of his mouth.
Once inside, go straight, find Princess Ruto, use her (or a small crate) to activate switches, then forget about her once she gets the Sapphire. Use the map to explore the whole dungeon, defeat the boss with your Boomerang and sword, and you're done. Use your Slingshot to kill enemies in this dungeon (if you don't have the Boomerang yet) and the Deku Shield to avoid getting shocked. The dungeon has been explained in more detail in a previous question.

You'll need to know how to get to Zora's Domain, this is how you do that: start by going to Zora's River - if you enter Hyrule Field from Kakariko Village, go left and follow the wall. When you get there, you'll need to Bomb the boulders and follow the river upstream to the waterfall. When you get to the waterfall, play Zelda's Lullaby and jump through it into Zora's Domain.

You'll also need the Silver Scale, so follow the stairs to the top and make a left; follow the hallwaay and you'll get to the top of the waterfall - now talk to the Zora and win the Diving Game to get it.

Now you'll need Princess Ruto's Letter in a Bottle - dive through the underwater tunnel to get to Lake Hylia. As soon as you get there you should see the Bottle in the water. Z-Target it, dive down and grab it; now go back to Zora's Domain through the tunnel and show that Letter to King Zora at the top of the stairs.

Half an hour later, he'll finally be out of the way lol and you can go by him. First, go put a Fish in your Bottle from the water below. Now go by the King and feed Lord Jabu-Jabu that fish to enter him; once you beat this place, you'll earn the third Spiritual Stone and be ready to go back to Hyrule Castle!

P.S. You only need to ask once =P
GOOD LUCK =D