After finding all of the Tears of Farore, you return to the forest with the Water Dragon's Scale. You can now swim underwater by tapping A and tilting the Wii Remote to change direction.
Swim into the Great Tree
There is a very large tree in the center of this area. There is water on the southeast side of the tree. Swim into that water and tap A to swim underwater, turing and rotating the Wii Remote to change Link's direction. Stay underwater to avoid the Quadro Baba up above. Get the amber relic here. You will find an opening in the base of the tree underwater. Swim into it.
Reach the Top of the Great Tree
Swim through the underwater passage, collecting air bubbles to avoid drowning. There will be a brief cut scene when you reach the interior of the tree.
Swim to the vines in front of you and climb up. Run onto the wooden platform, then use the Gale Bellows to make the platform swing around. Blow the Froaks away if they get too close. Don't bother trying to get onto the Bokoblin's platform. Instead, swing to the left to reach the ledge to the left.
Once you are on the ledge, go up and around. You will reach a tunnel with a bunch of keese inside. Up ahead you will find a Quadro Baba, but you can throw a bomb into its mouth and it will eat it and explode. Jump across and open the chest to receive a gold rupee, worth 300 rupees.
Now go back the way that you came, but don't go all the way down. After jumping down near the other end of the wood tunnel, you should be able to drop down to the other exit that you saw beyond the bokoblin's platform. This way you can exit without ever dealing with the bokoblin. Go outside.
You will be on some platforms outside of the tree. Climb up. You can't reach that Goddess Cube yet, so just continue on. You will reach some vines. Use the slingshot or beetle to get rid of the small spider on the vines.
Up ahead, you will encounter more vines. Use the beetle to get rid of these spiders, then climb up to reach a new entrance into the tree. You will hear a strange noise. Go inside.
There is a Wooden Shield Moblin here. It's actually really easy to get past it, and you don't even have to fight it. Just wait for it to rotate the shield and set it down, then, without using targeting, hold the A button to run up the shield and jump past the moblin. Go out through the exit beyond the moblin.
Up ahead, save at the statue. Then kill the bokoblins that attack you up the slope. Be sure to get rid of the blue one to keep it from summoning others. Get the amber relics from the hollow spots to the left. After killing the keese up ahead, walk up the ramp and Fi will mention the strange sound.
Climb the vines at the top of the ramp and watch the automatic scene. Use the slingshot or beetle to wake up the Kikwi. This is Yerbal, the Kikwi Hermit.
He will say "it's a secret to everybody," which is a famous line from the very first Legend of Zelda game for the NES.
He will tell you that Farore's Flame is in the care of the Water Dragon, who lives in the south of the woods. To open the gate there, you need to channel the power of the Goddess into the symbol carved on the doors, but you have to make the symbol whole first. To do that, you have to find the completed symbol elsewhere in the woods. He marks your map to find out where the completed symbol is. The Kikwi warns you to show good manners to the dragon.
Jump off of the tree and use the sailcloth to avoid getting hurt.
Find the Completed Symbol
The completed symbol is behind the Viewing Platform. Fi will tell you to memorize the shape of the symbol. It's a circle on the left with a small crescent moon in the middle and a larger crescent moon to the right of that.
Open the Gate
Put a beacon on the map to the south if you wish. It's at the very southern part of the map. To get there, when you get close you will find a watery area with a slope to the right. Cut the trees at the top of the slope and go through. The gate is pretty easy to find after that.
When you reach the gate, stand close to it and point your sword up to charge up the sword. You will get the option to draw. Hold the A button. You will notice that the missing part of the symbol is the circle on the left. Draw it slowly to make a nice round circle. It can be difficult to aim properly, so keep an eye on where the tip of your sword is.
Reach the Water Dragon
Once the gate opens, go through and go to the end of the path. Jump off of the edge to enter Lake Floria. A current will take you through the path. Inside, a strange creature will be afraid of you and back away slowly. Follow him. You will reach a wooden gate that the creature will go through. Shake the nunchuk to do a spin attack through the gate.
The creature will realize that you are an emissary of the Goddess. He asks you to help the Water Dragon. A human brought a bunch of monsters and attacked the dragon, but she was wounded and needs more sacred water in order to heal up fully. Follow the creature.
You will reach an area where the path to the next area is blocked by rocks. Do spin attacks into the Froaks to push them into the rocks. The froaks will explode and break the rocks. There is a silver rupee under the rock in the middle of the floor. After bombing the rocks blocking the way to the dragon, the creature will tell you to keep following.
You will reach a gate. To get over it, you have to do a spin jump. Talk to the nearby creature to learn how. Just swim down below and then shake the nunchuk while swimming straight up while close to the gate. If you did it correctly, you will spin jump out of the water and get over the gate.
The creature will swim through a narrow gap in the rocks. Use a spin jump to get out of the water. Walk up and save the game, then open the blue chest, which contains a Goddess Plume. Behind the chest you can see a Goddess Cube in the distance. You can easily walk over to it. After hitting the Goddess Cube with a skyward strike, go back into the water and follow the creature. Be careful of the green spiky things in the way.
Up ahead, you will encounter an enemy fish. Stun it with a spin attack when it charges toward you, then use another spin attack to kill it.
Swim toward the creature and you will reach a door. The creature will use his oddly-shaped head to unlock the door. Go through.
Climb onto the structure in the center and talk to the tiny dragon atop the statue. She is Faron, the Water Dragon. She wants to test you to prove that you are really the hero.
Find the Sacred Water
Fi will make it possible to dowse for the sacred water. If you don't have an empty bottle, you will need to get one. Before you exit, however, go around the room to find a blue chest in the back that contains an Evil Crystal. There is also a second blue chest in this area with a silver rupee inside. You will need to do a spin jump to reach it.
Use the exit to the woods that Faron showed you.
Strum the harp near the butterflies to find a gossip stone.
Be sure to push the log nearby to give yourself a shortcut. The sacred water is in the Skyview Temple, so you might want to just use the bird statue to go back to the sky, then dive back down to the forest and choose the bird statue near the Skyview Temple.
If you would rather walk, then jump down where you pushed the log. There is a Wooden Shield Moblin. To kill it, you can cut apart its shield, or you can run up the shield after it rotates it and sets it down, then hit it from behind. Be sure to run away if it's about to swing the spear. After its shield is gone, just hit it with your sword until it dies. Run up the watery slope. Dowse to be led to the Skyview Temple. If you encounter a missing rope, go around the other way, to the left (check your map to find it.) Use the log next to the tree to go up. The gossip stone here will tell you that you can collect glittering spores from sparkly mushrooms.
Go into the Skyview Temple. You can't dowse for the sacred water, but Fi will mark an X on your map. It's through the door that led to the boss of this dungeon.
There are tougher enemies here now. Go to the middle room. The door across the way is locked again. Go into the east side room. Don't bother with the staldra across the way. Swim underwater and crawl into the small gap on the east wall. On the other side, climb the vines and you will find the key in the dirt up ahead.
Return to the middle room and use the key on the locked door.
When you get to the room with the door marked on your map, use the beetle to drop a bomb onto the bokoblins across the way, then go across the rope. You don't need to unlock the door again, so just go through.
There are three stalfos here. Just pay attention to which way their swords are pointing to see the correct direction to slash the sword.
After getting rid of the Stalfos, go through the door to the Skyward Shrine. Use dowsing here to locate the spot where the sacred water is. It's at the base of a waterfall, so stand in the waterfall and scoop with an empty bottle to get the sacred water.
Outside, you might want to return to the sky and then dive back down to return to the statue near the Floria Waterfall. Then you can walk straight into the Water Dragon's room. Talk to her and she will open the waterfall for you.
Use a spin jump to get onto the ledge beyond where the waterfall was. Go inside.