~ Hyrule Field ~ 
Now that we have both the Iron Boots and Zora’s Tunic, we can enter the Water Temple. There’s a few goodies we can get along the way as well. First of all, use the Prelude of Light to go to the Temple of Time, then ride Epona to the northwest most portion of Hyrule Field. The tree closest to Lon Lon Ranch in this corner holds a secret. Place a Bomb beside it to reveal a hole.
Inside, kill the Blue Tektite and sink down to the bottom to claim the Heart Piece. Nice.
Now head to Lake Hylia, either by jumping the fences with Epona or simply playing the Serenade of Water.
~ Lake Hylia ~
Watch out for the Guays (crows) in the area, because after you kill them, they’ll reappear shortly afterwards…
The first Heart Piece we’re going to get is on top of the Lakeside Laboratory. You can get up there by either riding the Magic Bean Plant you could have planted as a child, or by playing the Scarecrow’s Song to make Pierre appear so that you can Hookshot to him. After using either method, climb up the ladder and find the Heart Piece that’s awaiting you.
Next, jump down and enter the Laboratory itself. There’s actually two goodies in here, but there’s only one we can get at the moment… Jump into the tank at the back and sink down with your new boots. Roll into the crate you find to reveal a Gold Skulltula. I didn’t know spiders could survive underwater… Use your Hookshot to kill it and claim the token.
Now, as you’ve already noticed, the water has drained out of the lake and some of the ruins are now more readily viewable. Simply follow the ruins to the lowest point of the lake and sink down to find a grated entrance to the temple. To open it, wear the Iron Boots and Zora’s Tunic and stand right before it, then use the Hookshot to hit the crystal thing right above the doorway. It’ll come out and slowly float to the surface, making the gate lift up as well. When you’re ready, enter the temple.
~ Getting The Dungeon Map ~ 
Before we begin, I need to explain something. This temple is generally considered the hardest in the game, puzzle-wise. Reason being, because you have to return to the same rooms multiple times and from different directions in order to progress through the temple. It’s a somewhat monotonous and aggravating temple if you don’t know where to go and what to do as well as when… The best advice I can give is, “try to go EVERYWHERE,” for every water level. You’ll see what I mean shortly…
Highest Level – East As you start off, float up from the entrance and emerge into the main room of the temple. Breathtaking isn’t it? These two Tektites in the center will continually reappear each time you enter the room, so be forewarned. First off, swim over to the entrance on your right (east). Follow the path, sink into the water and continue. You’ll shortly come to a giant red block. We’ll be able to push that block again from another direction much later, so forget about it for now and return to the main room.
Lowest Level – East (Ruto Room)
This time, sink down to the very bottom. You’ll probably have an encounter with the Spikes here. Use your Hookshot to kill them and, again, enter the west entrance (the one with the torches). As soon as you round the “S” shaped corridor you’ll witness a cut scene with, *gasp*, the adult Princess Ruto! She’s grown and she… doesn’t wear clothes…
After an awkward and surprising one-way conversation in which she claims to be your fiance, she will begin floating up. Take off your boots and follow her all the way to the top to find that she’s disappeared. =(
We won’t see her again for awhile so, again, forget about her as well. enter the door nearby.
Dungeon Map Room In this small room, you’ll be thrown into the midst of four Spikes all at once. try to kill them from afar to avoid taking damage. Should you decide to get close, Deku Nuts are easily the most effective weapon to stun them all at once. After they’ve all been killed, a large chest appears containing the Dungeon Map. Nice.
~ First Triforce Symbol And Key ~
First Triforce Symbol Go back to the previous room and stand in front of the Triforce symbol on the wall. In case you haven’t caught on yet, every time you see one of these symbols throughout the game, you’re supposed to play Zelda’s Lullaby (which is also in that shape). Doing so will cause the water to go down all the way to the floor! This is the first of three places you can change the water level that Ruto was talking about.
Jump down and you’ll see two torches against the door. Now that there’s no water, the single torch in the center of this small room is lit. Hmm… Either shoot arrows through the one torch to light the other two or use Din’s Fire. Once both torches are lit, enter the small room.
Shell Blade Room Inside, you’ll find a new enemy known as the Shell Blade. Either kill them from afar by Z targeting one at a time with either ranged weapons or your sword when their mouth is open, or just get close to all of them and kill them in one go with Din’s Fire. Snag the Small Key in the chest that appears, then return to the main room.
~ Optional Skulltula ~ 
Lowest Level – South Now take the south entrance (directly on your left), which leads to a dead end. But you’ll notice the floor has a crack in it, so whip out a Bomb and blow open hole in the floor. Sink down and you’ll immediately come across a Shell Blade. At this point, you can either kill it with your Hookshot, or take off your boots and swim over it. In either case, go up on the other side and pop out above the water.
Get on the small platform and step on the switch to raise the water level in this room just a little bit. Climb up one level and now the statue that was submerged has raised, revealing a Hookshot target. Zip across and kill the two Tektites. I find it easier to maneuver past them before facing off because I don’t have to worry about falling in the water.
After that, go stand in front of the gate and you’ll notice a crystal switch on the other side. You’ll have to use a Spin Attack to activate it, thus opening the door. Snag the Skulltula token and goodies, then return to the main room.
~ Small Key And The Dragon ~
Lowest Level – West
Next, go through the west entrance (on your left). By standing atop the block, you can push the red block all the way back until it falls into a hole and clicks in place underwater. Sink down and back up on the other side.
First Water Pillar Room In this small room, you need to get to the other side. Should you fall down into the pit, you can Hookshot your way back up. Smack the nearby crystal switch with your sword and jump onto the water pillar that raises up. Jump across to the other side and run right past the Tektite to the door.
Spinning Water Room This small room has a giant pool of water that spins around rapidly. Jump in and you’ll quickly see that the water will take you with it if you’re not heavy enough. There’s an iron dragon statue-like thing underwater that weaves in and out of the walls, try to land on its body in the opposite corner of the room from the door using your Iron Boots.
Once you’ve safely landed there and aren’t moving, hit the crystal switch in the dragon’s mouth with your Hookshot to open the nearby door. It’s only open for a few seconds, so Hookshot to the target on the wall in the alcove and run towards the door.
There’s two Shell Blades in here that make this process terribly annoying. You can either draw them out into the deeper water and kill them (usually takes multiple tries) or just avoid them as best you can. The latter is much faster and less aggravating in my opinion. To do so, just take off your boots as you’re approaching the entrance and float up into the small area.
Once you make it, climb up and open the chest for a Small Key. Nice. Now hit the crystal switch in here and swim back to the entrance. I like to use a Bomb to ensure I have enough time, but using your sword works just fine as well. Once you get back, go through the door.
First Water Pillar Room back in the room from a moment ago, kill the Tektite and Hookshot to the target across the way or simply shoot the crystal switch with an arrow. Work your way back to the main room. At the end, you’ll have to use your Iron Boots and Hookshot to get onto the platform.
~ Second Triforce Symbol And Hidden Small Key ~
Center Pillar
You should have two keys at this point. At long last, enter the locked door in the center pillar of the main room. Inside, run forward, turn around, a Hookshot up to the target on the side of the platform above you. Once you climb up, play Zelda’s Lullaby for the second Triforce to bring the water to the mid level.
Now, this is the part that stumps most people: In that little cut scene where the water’s rising, it showed that platform that floats rising, which reveals a hidden hole that you can sink down into. Get on top of either of the platforms here, equip the Iron Boots and step between them to land safely on the platform below (as opposed to the spikes). Sink down the hole.
Temple’s Flooded Basement Round the corner and you’ll find a lone crystal switch. Hit it from afar with your Hookshot, which will open up a gate above it, dropping down baddies to confront you. Defeat them one at a time while slowly inching your way forward until they’re all gone, which opens the gate above on the other side.
Float up and snag the Small Key from inside the chest. Nifty. Work your way back to the room where you just changed the water level and go through the door.
~ Getting The Compass ~
Mid Level – East (Compass Room) Now that the water’s at the mid level, there’s a few more rooms we can access. To help in finding all the keys, let’s snag the Compass (which is totally optional of course). Enter the east wing, (with the two lone jars,) and it’ll lead to some spikes. You could have actually gone here when there was water filling it as well, but there’s lots of Stingers underwater.
Anyway, Hookshot onto the platform across from the spikes on the floor, then turn around and Hookshot to the farthest target from you on the ceiling. This will take you all the way up. Now, we need to open the chest, but the crystal switch’s timer doesn’t last very long. Either lay a Bomb or shoot it from across the way to open the chest in time.
Return to the main room; just be careful when you jump down not to land on the spikes. 😉
~ Remember The Cracked Wall? ~
Lowest Level – East (Ruto Room) Next on the agenda: Blowing up a mysterious wall we saw earlier… Sink down to the lowest level and go back through the east entrance (with the two torches) where we met Ruto. Take off your Boots and float up, where you’ll find a cracked wall all by its suspicious self. Blow it up and snag the Small Key inside the little treasure chest. Go back to the main room.
~ Third Triforce Symbol ~
Mid Level – West You should have three keys at this point. Go through the locked door on the west side.
Here you’ll find another water pillar that’s obviously activated by the crystal switch across the room. Before jumping for it, walk near the water pillar to lure a Tektite from above. After killing it, use either a Bomb or Arrows to activate the switch and go up.
~ Getting The Longshot ~
Highest Level – West
Now, you should have two keys at this point. If you don’t, you’ll have to change the water levels a couple times and refer to previous points in the walkthrough to figure out which ones you missed. Anyway, if you do indeed have two, enter the locked door on the west again at long last.
Waterfall Room Inside, you’ll find an enormous room with a huge waterfall. First of all, kill the two Keese before they brew any trouble. Then jump down to the lowest platform directly below you. You’ll probably notice there’s a Skulltula on the wall that’s too far to get to. We’ll deal with that later. Anyway, jump to lone stationary platform near the bottom on the right if you think it’ll be easier for you.
Statue And Tektite Room In this room, you’ll have to hit the crystal switch in the center of the room with your Hookshot to raise and lower the water level repeatedly. By raising it, you’ll make the statues float up, revealing targets. Should you fall in while the water is low, you’ll have to equip the Iron Boots and hit the crystal switch with your Hookshot to get back to the platforms. First of all, I suggest raising the water, then luring the Tektites over to the starting platform where you can kill them off. Now, to the actual puzzle:
-Raise the water. Hookshot to the next platform (clockwise).
-Lower the water. Hookshot to the target on the left side of the next platform. Climb across the statue head.
-Raise the water. Hookshot to the last platform.
-Lower the water. Climb on top of the head of the statue. Raise the water again to go up.
Kill the two Blue Tektites up here, then kill the Like Like across the spikes. You can do so with a Spin Attack or Bombs. Hookshot the target on the ceiling to appear on the other side. Be sure to grab the goodies in the jars, a mini-boss is up ahead.
Room Of Illusions This is one of the coolest rooms in the whole game. It looks like an endless sea of water, with bits of ruins and a single tree in the middle. If you walk along the edges of the “room” though, you’ll find there’s invisible walls that clang like metal when you slash them with your sword, so you are still confined. At first, it may seem like nothing, so walk over to the opposite door and turn around. You’ll see something next to the tree in the middle…
Dark Link
This battle can be intimidating at first, but after you begin seeing the patterns in his attacks and simply avoid the moves that cause him to react, he can be quite easily defeated. Basically, he mirrors your every movement at first, but then gets more aggressive as the battle progresses.
Avoid using the Jump Attack (Z + A) and stabbing with the Master Sword (Z + B + Forward). Each of those cause him to counterattack, not that regular slashing doesn’t, but those two are guaranteed to fail every time (unless you miraculously catch him at a good time right after he attacks, very rare, not worth it).
Z targeting: More safe, can sometimes trick him. No targeting: Risky, tend to take damage yourself at the same time. Much faster.
This battle is quite memorable and hard if you only use the Master Sword and tricks to defeat him. If you want this to go quick or are running low on life, you can always just use other attacks, seeing as he ONLY has the Master Sword, you can take advantage of that. In other words: Din’s Fire or the Biggoron’s Sword. The larger sword + stab is very effective because he doesn’t have that same stab counterattack. Z targeting and just regular slashes are also very effective.
If you’re out of magic and don’t have the Biggoron’s Sword, your best bet is to either have no Z targeting and try to inch your way along his side while you slash continually. Otherwise, to Z target and angle your attacks with the Analog Stick to try getting past his slightly delayed attacks (just don’t stab with the Master Sword). It does work, it just takes a little persistence.
After you’ve defeated him, the room’s illusion will cease and it’ll revert to normal as well as open the next door. Spooky.
Longshot Room Open the large chest to find the Longshot! With that in hand, stand next to the Time Block on the other side of the chest and play the Song of Time to remove it. Fall down into the cavern below.
~ Don’t Get Sucked Into A Vortex! ~
Raging Water Cavern This long, twisting corridor is filled with rushing water and “vortexes” that will suck you in and make you start the room over again if you’re not careful. There’s two ways to go about this: use the Iron Boots, or risk swimming. It may seem logical that using the boots is by far the better option, but because of the way the ground can make you slip (some of the angles make you slide down repeatedly) it can actually be detrimental to your progress. I suggest swimming for the most part, taking it slow, the pressing B to swim fast when you need to.
To start off, jump in the water and head to the end of the first section, hug the left wall and make it past the first vortex.
At the next corner, put on the boots and use your Longshot on the Gold Skulltula on the wall. Take off the boots and round the corner, hugging the right wall.
Ahead, there’s two vortexes. If you use your Iron Boots here, it’s very hard not to get sucked in. Swim along the right wall towards the little ledge with the two jars. I like to climb up and get my bearings.
Now, our next objective is to swim across to that little platform opposite, between you and the closed corridor. I suggest jumping into the water close to the platform in the corner with the two jars, waiting until you’re floating safely on the surface, then swim between the raging waters and climb up. It’s really pretty easy. If you’re worried about it, use the Iron Boots to get close, then take them off to climb up.
Whip out your Fairy Bow and shoot the golden eye switch on the wall across from you. This opens up the doorway for a few seconds. Jump across and open the chest for a Small Key.
Jump down into the spinning room with the dragon we tackled earlier, work your way back to the main room, just like we did before.
~ Last Small Key ~ When you return to the main room, the water should be at its highest point. To the north is the boss room, but we can’t get there since we don’t have the Boss Key yet. Before we change the water level, enter the west door, which leads back to the room with the descending platforms on the waterfall you had to Hookshot up through.
Now that we have the Longshot, you should easily be able to snag the Skulltula on the right wall. Return to the main room.
With Longshot in hand, we can finally access two more rooms that you’ve probably already investigated with little results. The first one we need to inspect is on the second level, so sink down to the bottom of the main room and go through the east corridor (where we met Ruto), float up and change the water level to the bottom.
Next enter the center pillar, Longshot up and play Zelda’s Lullaby yet again. Before we exit through the door, use your Longshot to snag the Skulltula token hiding above you.
Back in the main room, go and face the south corridor (with the golden eye switch and the iron grating). You may want to lure the Blue Tektites down and kill them before you tackle this. In any case, shoot the golden eye switch with an Arrow to lift the grating temporarily. There’s only enough time to Longshot in (you couldn’t reach before)
Go down the corridor and you’ll find the red block we pushed at the beginning of the temple. Push it into the hole and go right to find a chest containing a Small Key.
We can’t exit the way we came in, so instead, go the other way and Hookshot up to the top level and return to the main room.
~ Getting The Boss Key ~
Main Room (North) You should have two Small Keys at this point. The second room that’s now opened to us is on the bottom level (but you don’t need to change the water level). Sink down and enter the north corridor (the sandy area with the ditch and two Spike enemies). Sink down and float back up to find yourself in a room with a spike wall blocking the way to the door on the other side. Turn around and climb onto the ledge, then Longshot the target on the other side of the room and enter the locked door.
Rolling Boulder Room This room is filled with some crazy strong flowing water that zig zags through the room with a couple vortexes, six Blue Tektites and two rolling boulders. There’s two ways to go about this, you can try to get across and sneak past the Tektites and Boulders, or you can lure the enemies to your side by either swimming out and back or shooting them. Luring them is safer, but the more I play through the game, I just get impatient. Swimming across is quite easy, just stay on the right side near the end and swim under the Tektites. If you start heading for the vortex, just slip on the Iron Boots.
Whichever method you choose, once you make it across and enter the next door.
Stinger Room To start off, kill the Stingers in this room. If you take too long, they can actually begin flying around the room (glitch?) so I suggest using Z targeting to shoot them with Arrows. Once they’re dead, jump down into the water.
Okay, so first understand that this room has a walkway that’s “U” shaped, it goes behind the wall, which you can obviously blow up. There’s two places to do so, making the full circuit. Inside, you’ll find a stone block that’s just begging to be pushed and pulled. Use both entries to do just that and get it to land on the switch in the water.
This will raise the water level in this room, allowing you to enter the next door.
Second Water Pillar Room We treat this room the same as the last one, except there’s more water pillars and Tektites to deal with. You may want to lure them off first by either jumping down and getting close to the other side, or shooting them with arrows. One of the differences in this room from the last is that the timer that activates the pillars also opens the door on the other side.
Rolling Boulder Room Now that we’re up in one of the alcoves where the boulders come from, we can get a Skulltula. Sneak out to the edge and snag the token on your right. Wait for the boulder to pass, equip your Iron Boots and jump into the water, go towards the waterfall and sink into the deeper water.
Round the corner slowly, as there is a Shell Blade right around the bend. Kill it with your Longshot. After you kill it (or fail to do so and get frustrated) take off the boots and float up. Enter the locked door, using your last Small Key.
Open the pretty chest to find the Boss Key. Nice!
~ Getting To The Boss Room ~
Main Room At long last, we’re ready for the Boss Room. Go around making the water to the highest level, then you can finally Longshot onto the target of the dragon statue in the northern part of the room. Fill up your bottles with Fairies in the jars nearby if you like, then enter the door.
Spike Trap Corridor In this small room, you’ll have to run by the Spike Traps. Just stay on either the left or right side and run straight. If you slow down at all or roll, you’ll slide all the way down, most likely getting hit in the process. Once you get to the top, head on through the menacing door.
Boss Room As soon as you enter, Navi will exclaim that the water isn’t natural. Well, that’s certainly comforting. Jump onto one of the platforms in the middle to begin the boss battle.
Giant Aquatic Amoeba, Morpha
Alike the last boss, this one deals out quite a bit of damage should you accidentally get caught. This boss is rather simple: it really only consists of a single orb that controls the water in this room (in the form of tentacles that try to grab you). You can easily tell where the tentacles are coming from by the noises they make.
To avoid taking loads of hurting, simply stay a good distance away from each tentacle as soon as you see them beginning to appear. It’s pretty easy to stay out of their range. Wait until the nucleus attacks through a tentacle, use Z targeting and Longshot it. Make sure there’s plenty of room on the ground in front of you for it to bounce around, lest it fall back into the water as soon as you get it! As soon as you do get it, smack it with your sword, quick-like.
After several hits, it’ll summon two tentacles at once, and eventually three. Repeat the processes just like you did before. If you’d like this to be a challenging experience, stay ONLY on the four platforms in the water. If you’d like it the other way… just hang out in the corner where it can’t reach you… *GASP!*
After its been defeating, Morpha will explode into a pile of water, leaving the rest of the possessed water in the room to suck up to the ceiling and trickle away. Pretty sweet little cinematic really.
Jump down and be sure to grab the Heart Container before entering the glowing circle.
~ Water Medallion ~
Temple of Light You’ll then appear in the Temple of Light, along with Ruto. Too bad she doesn’t explain why she disappeared, though the bad guy had her!
Anyway, she’ll ramble about your “engagement” and how you’re looking for Zelda before giving you the Water Medallion at long last.
~ Fire Arrows ~
Lake Hylia You’ll appear back in Lake Hylia along with Sheik, who has more poetry to recite. After a quick glimpse around the lake as its filling back up with water, she’ll disappear.
Now that we have the Longshot, we can do something we couldn’t before. Atop the tree on this island at night is a Gold Skulltula. Hookshot onto the tree itself above the branch (at an angle). Once you get up there, play the Sun’s Song to make it night.
After getting the Skulltula, jump down and stand on the brown platform. It says to “shoot for the morning light,” and seeing as it’s morning, use an arrow to do just that. A short clip will ensue, revealing the Fire Arrows out on the small island. Swim out and grab them.
~ Let’s Go Fishing ~
Lake Hylia
At long last, with water filling the lake, we can return to the Fishing Pond. You probably visited it as a child, but if not, it’s in the northeast chunk of the map, the only other building in the area, off by its lonesome in the water. (How do they expect people to easily get there anyway?)
It’s actually possible to go here earlier, using the Scarecrow’s Song while the lake is still drained, but I figured I’d wait until most people would play this mini-game.
Fishing Pond
After paying the man behind the counter 20 Rupees, you’ll be given a fishing pole and can fish for as long as you like. This particular mini-game can easily lead to hours of fun trying to find the biggest catch.
Press A to cast and reel in. Press B to wiggle and use the Analog Stick to pull the line in a direction. Once you’ve found a fish you’d like to snag, Z target it, then use A to cast. Use it in midair to get it closer to your destination if it goes too far.
Let it get close then use a combination of B and the Analog Stick to attract the fish. Just do nothing if you get the wrong one and it’ll let go. If you miss, use A + R to reel in fast and start over.
That’s all the basics, just remember: DON’T SCARE THE FISH! If you do, they all run to the deep water. The other tip I can give you is that all the fish start in a specific spot. The biggest one is by the arched log, close to the three sticks sticking out of the water.
If you catch a fish that’s fifteen or more pounds, you’ll win the Gold Scale. With that in hand, leave the Fishing Pond and go to the Lakeside Laboratory (only other building in the area).
Jump into the pool here, dive down and touch the bottom. The old guy up top will holler at you and after speaking with him in person, he’ll give you a Heart Piece. Nice.
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