The infamous Water Temple is the cause of frustration for many gamers, especially in the original game. To access all the levels of this multi-layered temple, you must change the water level frequently and constantly equip and un-equip the Iron Boots. The 3DS edition includes some modifications to make the dungeon a little less difficult, but it can still be confusing and frustrating without guidance.
For The Legend of Zelda: Ocarina of Time 3D on the 3DS, a GameFAQs message board topic titled 'What does the Triforce of Courage exactly do?' Zelda gets the Triforce of Wisdom and Ganondorf gets the Triforce of Power when he tricks Link to open the door of time, he uses his magic to get the triforce, but it splits into 3 parts and he is. Ocarina of Time. After Link opens the Door of Time and removes the Master Sword from its pedestal using the Spiritual Stones and the Ocarina of Time, Link is sealed away within the Sacred Realm for seven years. Ganondorf uses this opportunity to enter the Sacred Realm and claim the Triforce as his own. Empires and allies cheat codes.
Get used to this central room, because you'll will return here several times before completing the dungeon. If you have Faeore's Wind, keep re-setting the warp point to here, to save some time. The first thing you must do is swim over to the right platform, go through the short hallway, and dive into the water here, using your Iron Boots to move around underwater. In this particular tunnel is a block that you must pull out until it can no longer move. This is important for later and will save you some unnecessary backtracking.
Return to the center room, throw on the Iron Boots and sink down to the very bottom. Run through the passage flanked by two unlit torches to meet up with Princess Ruto. She swims upwards to show you the first place you can change the water level.
Remove your Iron Boots to float all the way to the top after Ruto. Ruto is no where to be found, but there's a Triforce symbol on the wall. That's your cue to play Zelda's Lullaby to force the water level lower. Go through the door to encounter some brand new enemies that can be killed easily with the Hookshot when they are in rock form. Grab the Dungeon Map from the chest that appears.
Exit the room and jump back down to the spot where you met Princess Ruto. Shoot arrows through the lit torch to light the two unlit torches on either side of the door (Din's Fire will also work). Go through the unbarred door to a room inhabited by Shell Blade creatures. L-target one, wait until it opens its shell up, then fire at it with your Hookshot to kill it instantly. After you kill all three, grab the Small Key.
Return to the central room and go to the blocked entryway on the opposite side. Push the block until it drops and wade through the tunnel to the new room. The diamond switch creates a water spout that you can use to cross the gap to the other side. There's a whirlpool in the next room; jump into it. Put on your Iron Boots again and stand on the pipe to the right of the stone dragon's head. Use your Hookshot to hit the diamond switch resting in the dragon's mouth, then quickly look right and hit the Hookshot target in the underwater tunnel to quickly pull yourself over. Watch out for the Shell Blades and float up to the mini-room. Take the Small Key from the chest before hitting the switch again to re-open the gate.
Return to the main room of the temple and go through the only locked door on the bottom floor (towards the center of the room). Walk straight forward, turn around, and Hookshot up to the Triforce symbol. Play Zelda's Lullaby to raise the water level of the dungeon halfway.
Equip your Iron Boots and sink down, being careful to avoid the spikes. You'll see an opening in the floor that was previously covered with a block. Sink to the bottom of the hole to enter an underground room. Strike the diamond switch to unleash a bunch of Shell Blades and Spikes into the room. Eliminate them all using your Hookshot to unlock a gate in the right-hand corner, leading you to a Small Key.
With the temple half-full, go to the central room and look for a platform holding two pots. Hookshot over to it and continue to follow the Hookshot targets to a small room with a treasure chest. Stand in front of the chest and fire the Hookshot into the diamond switch across the room. Quickly pop open the chest to gain the Compass. Return to the central room.
At this current water level, head to where you first met Ruto and float up. Use a bomb to open the cracked wall to get another Small Key. Return to the main room and go through the locked door on the same floor as the current water level. Here, you'll need to stand on a water spout and shoot the diamond switch from the water spout using either arrows or the Hookshot. Go through the door leading back to the central room. Immediately to your right you'll find another Triforce symbol, this one causing the water level rise completely. Play Zelda's Lullaby and head through the locked door on the west side of the room.
Take out the Keese, hop down to the stationery platform below, then onto the moving platform below that one. Wait until you're pretty low on the moving block, then use your Hookshot to aim for the targets on the other moving platforms. Continue to Hookshot your way from platform to platform until you can reach the locked door.
Enter the next room. The switch in the middle controls the water level of this room only. Take out the Blue Tektites with arrows, the shoot the diamond switch. When the water level rises, the dragon statues also rise to reveal Hookshot targets. Hookshot over to the target to the west, then shoot the switch to lower the dragon heads. Hookshot to the target to the north, climb over the dragon head, then hit the switch again. Hookshot over to the last dragon head and hit the switch yet again. Stand on top of the dragon head and hit the switch one final time to reach the alcove above. Kill both Tektites, and take out the Like-Like with your bow, making sure to fire your arrows over the spikes (they won't go through them). Hookshot to the target above where the Like-Like stood and head through the door.
As you cross the expansive area in the hope of going through the door on the opposite side, you are stopped dead in your tracks by a barred door. Turn around and walk toward the center island to trigger a battle with your doppelganger, Dark Link. (If he doesn't appear, walk over the small island, then back to the barred doors, then back to the small island again).
Dark Link mirrors your every move. The best way to defeat him is to never use Z-target and slash away. Biggoron's Sword will work especially well, if you have it. After several hits, Dark Link will finally fall.
For a more in-depth description for defeating this mini-boss, see Shadow Link for more information.
Go through the north door. Take the Longshot from the chest, an upgraded Hookshot that reaches twice as far. The Song of Time song will make the blue block behind the chest disappear, allowing you to drop down into the room below. At the river, you can use your Iron Boots to navigate the treacherous river, but it's much easier to swim through it. Avoid the whirlpools or they'll take you back to the beginning.
Quickly heave yourself up onto the small platform on the left (the one without the pots). Hit the golden eye with an arrow to temporarily open the gate and tag the treasure chest with a Longshot to quickly cross over. Inside the chest is a Small Key. Continue through the hallway to reach a familiar room. Return to the central chamber.
The next step is to bring the water to mid-level once more. First you'll need to drain it completely from the room above where you met Princess Ruto, then raise it at the second Triforce symbol in the central structure.
Back in the main room, the south doorway is blocked off by a black metal gate. Fire an arrow into the eye below the doorway and shoot the Hookshot target to cross over before the gate closes. Hopefully you took the advice at the beginning of this Walkthrough and moved the block from its initial resting place, because now you can just push it off to the side to access the room behind it. If you didn't move it, you will need to head to the third floor (full water level), pull the block out, and return to this point. The chest inside gives up a Small Key. Since the way you came in is blocked by the gate, you will need to return to the central room via the route you took when you first moved the block, or via Faeroe's Wind.
Sink down to the bottom and enter the passage to the north. Remove the Iron Boots and climb onto the ledge opposite the spikes. Use the Longshot to sail over the spikes and reach the locked door. The door brings you into a room separated by a large pool in the middle filled with Tektites, whirlpools, and boulders rolling into it. They are certainly treacherous waters to cross, but you can make the crossing slightly easier by killing as many of the Tektites as you can with arrows. Make your way to the other side and go through the door.
In this room take out the Stingers with your Longshot. The walls on the southeast and southwest corners can be bombed, revealing a small connected corridor with a huge block in it. Enter the passage from the southwest corner and push the block as far as you can. Now enter the corridor from the southeast corner, and pull the block. Enter from the southwest corner again and push the block into the water so that it depresses the switch. This raises the water level of the current room, allowing you to reach the door on the west side. In the next room, pick off the Tektites on the opposite side before stepping on the switch to activate the water spouts. Use these to traverse the wide gap, then enter the door.
Wait for a boulder to pass, then jump into the water to the right and equip the Iron Boots. Take out the lone Shell Blade with your Longshot, and float up to the final locked door. The Boss Key awaits you in the next room. If you need them, there are fairies in the pots in this room. Return to the main room.
The boss door is located on the 3rd floor, so you'll have to make the short trek back to the third Triforce symbol (2nd floor, west door) to completely flood the temple.
Once the water level is at its highest, use the Longshot to cross over to the dragon statue on the north side of the room, and enter the door. The last obstacle before the boss door is a relatively sharp incline with moving spikes. Running up this incline must be timed appropriately since any damage or movement other than running up will only cause you to slide back down. When you reach the top, enter the door to the Boss Chamber.
The red nucleus of this amoeba is the boss' weakpoint. Simply stay on the surrounding platform rather than the platforms in the middle of the water (be wary of the spikes on the side). Morpha follows a very rigid pattern, in which it basically swirls around in the water and summons tentacles. Morpha will try and grab you with these tentacles, so try and stay far enough out of its reach.
Fire your Longshot at Morpha's nucleus. Because the nucleus moves around a lot, the best times to snare it is when it travels back and forth through the outstretched tentacles. After you pull the nucleus close to you, deliver a few blows with your sword. After a few sucessful hits, Morpha will summon two or three tentacles at a time, but only one will contain Morpha's nucleus. Repeat this until Morpha is vaporized.
For a more in-depth description for defeating this boss, see Morpha for more information.
Collect the Heart Container from the center of the room and be transported to the Chamber of Sages to receive the Water Medallion from Ruto.
When you return again to Lake Hylia, you will encounter Sheik and watch the lake be refilled.
Read the plaque near the Lake Hylia warp point for a hint about shooting into 'the morning light'. Look toward the island with the two epitaphs, play the Sun's Song to manipulate the rise and fall of day. At the first break of dawn, fire an arrow into the rising sun to forge Fire Arrows from the sun's power. Swim across to gather them.
While you're still here in Lake Hylia, you might as well tie up any loose ends here. Make sure you've gotten all the Gold Skulltulas from the Water Temple. There's also a Gold Scale to be won from the Fishing mini-game, if you haven't done so yet.