In Oracala of Time, I have the first two stones and I'm at the lake, but..

Yeah, you definitely need a clue. To start on the quest to get Zora's Sapphire, you have to follow the Zora River to Zora's Domain. You'll also need to have a Bomb Bag.

From Hyrule Field, outside Hyrule Castle, follow the Zora River and enter the next area.
Bomb the boulders, jump diagonally across the river, run past the Octorok, jump across the river, jump diagonally to the left, run past the monsters, pull yourself up, run up the slope and make your way up to the waterfall. Use Zelda's Lullaby to get through.
In Zora's Domain, talk to the King of the Zoras, then go to the left and play the waterfall diving mini-game. Win the Silver Scale and return to Hyrule Lake (via square hole in water at Zora's Domain).
At Hyrule Lake, dive for the glass bottle, and return to Zora's Domain.
Show this to the Zora King, enter the area behind him, drop a Fish in a bottle in front of Lord Jabu-Jabu and enter the dungeon.

In the dungeon, you first need to find Princess Ruto (as she is used to weigh down buttons when no crates are nearby), then you can look for the Boomerang (in one of the chambers north of the main chamber).

The Third stone is not found at Lake Hylia. However while you are there you should get something that you will need to complete your taks of getting the third stone. Go down to the waters edge where you see a couple of pillars, if you get in the water and look down you will see a bottle. Z-target this bottle and then dive to pick it up. Next head to Zora Domain and show the note in the bottle to King Zora. He will give you the task of rescuing Princess Ruto who is located inside Lord Jabu-Jabu. So with your new empty bottle you should go scoop up a fish and then go behind King Zora leading you to where Lord Jabu-Jabu is. Empty the fish in a bottle right in front of Lord Jabu-Jabu and he will open his mouth and suck you and the fish inside. The third stone is located inside of him along with Princess Ruto but from here on you should be able to do just fine. Good luck!!!

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!

If you need more help, just ask =D

If all that other stuff doesn't help I found a video walkthrough that will probably help you out, it starts out inside Lord Jabu Jabu's belly and shows how to complete everything and how to get the spiritual stone.