A WATERY GRAVE
When you first enter the temple, you'll still have the Iron Boots on. Take them off and float up to come to the large main room, which at the moment is flooded to the top. Don the Iron Boots again and sink to the bottom of the main room. Look out for the sea urchins here; a single hit from the Hookshot will send them packing, or use the Shield to defend against them. When the urchins have their spines retracted they'll be very still, so that's a good time to hit them.
Anyway, after you sink to the bottom of the main room look for the passage with two unlit torches marking it. Enter to meet Princess Ruto, saved from the Ice Cavern by Sheik. Ruto will explain that there are three places where you can change the water level, then rise up and out of sight. You won't see Ruto again for the rest of the temple, so don't worry about going fast. After Ruto vanishes, don the Kokiri Boots and swim to the surface.
Go through the nearby door and knock out all of the sea urchins to make the chest containing the Map materialise. Go back through the door, and on the wall will be a Triforce symbol with an inscription. Play Zelda's Lullaby here to drain the water to the very bottom, then jump back down the hole you swam up (don't worry, you won't take damage). Here, use Arrows or Din's Fire to ignite the two torches and open the door. In this room, you must knock out all of the clams to reveal a Key; hit the tongue with the sword or the Hookshot when the clam opens his mouth to knock him out. This is very difficult, but if you master this technique you've got half the temple finished. Once you have the Key, return to the main room.

Go though the passages which is directly opposite the one with the torches. Strike the Crystal Switch to make a column of water rise up, then use it as a stepping stone to reach the other side of the room. Remember, the switch is timed. When you reach the other side, you'll be in a room that has a pool of water when a strong current. Using the Iron Boots, sink down and stand on the purple dragon's tail, then look around for the dragon's mouth. Inside the dragon's mouth is a Crystal Switch, so hit it with the Hookshot to raise the portcullis briefly. Grapple the target and shed the Iron Boots to reach the surface in time, and ignore the clams. Up here you'll find a Key, and after you recover it return to the main room.
In the centre of the main room, there is a large pillar and on one side of the pillar is a locked door. Enter the door and use the Hookshot to reach the floor above. There is a Triforce symbol set into the wall, which will raise the water to half-way when you play Zelda's Lullaby to it. When the water raised, a pontoon floated to the top: don the Iron Boots and sink down, being wary of the spikes, and go down the passage underneath the pontoon. This is probably the hardest passage to find, and it was reaching here that got me stuck!
Proceed along the passages here until you come to the room with the lone Crystal Switch. Activate it with the Hookshot, but don't stand anywhere near it! because a heap of clams and sea urchins will be released when the grille above opens. Eliminate all of the hostiles and another grille will open; it's in the corner of the room, opposite the entrance and Crystal Switch. Float up there and you'll get another Key, so backtrack to where you rose the water level and float to the top of the water. There's a door here that'll take you back to the main room.

Upon your return to the main room, don the Iron Boots and sink back down to the bottom of the main room and go through the passage marked by two torches. Float up again, but you'll only go part-way and come to an obviously weak wall. Bomb the wall to reach (guess what?) yet another Key. Return to the main room and float up to the second floor.
Go down he passage which has lots of pots around it, grappling the Hookshot targets as you go. You'll come to a room with a chest surrounded by water and a Crystal Switch; stand next to the chest so that you can open it as soon as possible, the hit the Crystal Switch with an Arrow. Open the chest to grab the Compass, then return to the main room.
Stay on the second level, and look around for the locked door. In this room, stand near the water and wait for the Tektite to jump down so you can take him out. Once the Tektite is down, stand on the water and hit the Crystal Switch with the Hookshot. This will take you up and you can jump onto a stable platform, proceeding along the passage to an alcove in the main room. Along the wall here is a Triforce symbol, so play Zelda's Lullaby to raise the water to its highest point.
Look for the tunnel which has a block you can move. Pull the block towards the main room as far as it'll go, then go through the locked door directly opposite here. Ground the two bats, then carefully jump down onto the moving platform. When the platform reaches its lowest point, grapple the Hookshot target on one of the platforms on the far side. Do this quickly, before the moving platforms send you into the bottomless chasm. Keep grappling the targets to climb up to reach the locked door on the far side of the room.

This room is interesting: first, hit the coloured Crystal Switch to raise the dragon statues (and the water level, so be careful of Tektites). Using the Hookshot, grapple the statue's target and reach the other platform, then hit the Crystal Switch again. Look around for a Hookshot target in the wall, and grapple that. Get into Hookshot range to hit the Crystal Switch again so you can cross the water to the final platform, then hit the Crystal Switch again. Climb on top of the last statue you grappled, then hit the Crystal Switch to raise it and reach the door. Phew!
Don't breathe yet, since you must battle some Tektites. Once they're knocked out, I recommend you destroy the Like Like on the far side of the spikes with Arrows. When you're ready, use the Hookshot to grapple the target in the roof and get on the far side of the spikes. Go through the door to encounter a large, bright natural-looking room. In this room, run straight for the far side to encounter a barred door. Now turn around and run straight for the tree on the island to meet your foe, Dark Link!
Dark Link is an annoying boss, since he has all of Link's sword and shield moves and can easily duck all of the projectiles. People say that you should defeat him using the Hammer, but I fail to see what makes that so easy. If you've got the Magic Power, repeated use of Din's Fire works wonders. The easiest way to defeat Dark Link is with the sword (would you believe), but there's a catch.
When Dark Link appears, move away from him and, without locking Z-Targeting onto Dark Link, perform repeated Jump Attacks. You'll hear Dark Link grunt as he mimicks your attack, but after a few he'll stop mimicking them! Now, face Dark Link without Z-Targeting him. Strike him once with the sword when he gets into range, then turn around to face the camera. Dark Link will appear behind the real Link, so facing the camera will make sure Dark Linka appears within your view. When Dark Link reappears, repeat the attack from the top.
After Dark Link is down, the room will change to match the rest of the temple and you can go through the barred door. Open the chest in this room and you'll have the Longshot. Now, go behind the Longshot's chest but stay on its platform and play the Song of Time to dissolve the Time Block and reveal a manhole. Jump down the hole.

In this serpent-shaped room, you must travel with the current while avoiding the whirlpools. Getting caught in one will cost you one heart's health and return you to the start. An easy way to get through it is by donning the Iron Boots and walking along the ground, getting into a position where you can avoid the whirlpool's pull. Work your way to the stable platform without the pots and climb onto it.
Set the Bow and Longshot to C. Hit the yellow Eye Switch here with an Arrow, then grapple the chest behind the rising portcullis with the Longshot. Open the chest for a Key, then follow the passage to return to one of the earlier rooms. Take the dry road to return to the main room, then return the water level to the half-way mark.
To do this, first use the Iron Boots to sink to the bottom of the main room. Go through the passage with the torches, then float up and play Zelda's Lullaby at the wall's Triforce symbol to drain the water to the bottom. Now drop down and return to the main room, then go into the central pillar. Climb up to the second floor by grappling the targets with the Longshot, then playing Zelda's Lullaby on the Triforce symbol in the wall. A nearby door returns you to the main room.

Look around here for the blocked passage with a yellow Eye Switch below it. Hit the Eye Switch with an arrow, then grapple the target with the Longshot to get to the other side of the portcullis in time. Proceed along the passages and you'll come to a block you can move....the same block we pulled earlier. Move it out of the way and you'll reach a chest with another Key. Return to the main room, don the Iron Boots and sink to the very bottom.
Using the Map, determine which passage you haven't yet explored and go down that route. Grapple the target to reach the locked door and go through it. In this room, destroy the six Tektites with Arrows before swimming to the far side of the room and going through the door. Here, knock out all of the flying stingrays before using the sword to find two weak walls, which should be bombed.
By bombing the walls, you revealed a movable block. Push it so that it falls onto the hold-down Floor Switch and keeps the water level raised. Float to the top, swim to the door and go through it. In this next room, get rid of all the Tektites before activating the Floor Switch; jump accross the water stepping stones to reach the far side, remembering you must get through the door before the Floor Switch's timer runs out.

In this next room, you'll see a waterfall here and a rolling boulder will pass now and again. Get to where the rolling boulder falls, and you can sink down the water there with the Iron Boots on. Follow the passage to the locked door, go through and you'll come to the Boss Key. Shatter the pots here for some fairies, then return to the spot where you saw the rolling boulder.
Go along the boulder's path and you'll come to the room with the six Tektites. From here, backtrack to the main room and float to the surface. Go through the door that leads to the Tektite guarding the room with the rising water elevator. Retrace your steps along this passage, playing Zelda's Lullaby on the Triforce Symbol when you reach the alcove in the main room. With the water back to its highest point, float to the top level and look around for a passage which can only be reached by using the Longshot to grapple the target on a dragon statue.
Once you reach the right spot in the main room, shatter the pots for fairies then go through the door. Here, you must run up the steep slope without touching any of the switchblades, which is difficult because if you get hit or don't run at full speed, you'll slide back down tot he start. To reach the top, go all the way over to the left or right side, then wait for the very first switchblade to move out of the way. When it's gone, run to the top and open the boss door.
Navi will warn you that the water in this room isn't pure. Jump onto one of the four platforms in the pool, and the keeper's cinematic sequence will begin. You've just come through what is easily the longest temple in the game, so feel pretty pleased that you've reached the keeper:

MORPHA: Giant Aquatic Amoeba
amoeba (say a-mee-ba) noun, plural is amoebae or amoebas, also spelt ameba; a microscopic, unicellular animal which moves by changing its shape and reproduces by simple division into two parts (source: Heinemann Dictionary). And wasn't this guy off making more trouble in James Cameron's The Abyss?
Morpha's only vunerable area is the cell in the pool of water, which you lock onto with Z-Targeting. You must pull the cell out of the water with the Longshot, then hit it with the sword. Unfortunately, Morpha moves too fast for you to just lock-on and fire; you must wait for the cell to slow down before you can grapple it.
Morpha attacks by generating a tentacle of water, then trying to grab Link and toss him around the room. To avoid the tentacle, you simply have to run to the other side of the room, being wary of the spikes along the room's perimeter. As Morpha extends his tentacle, the cell will be pulled up as well. When the cell moves up the tentacle, lock onto it with Z-Targeting and use the Longshot to grapple it and pull it towards Link. You have several seconds to grab Morpha, so be patient and wait for the right opening.
Once you've pulled Morpha out of the water, hit him with the sword. You can only make one attempt at hitting the cell, so I recommend using Biggoron's Sword. Morpha will then bounce around wildly, getting back into the water to start another attack. If Morpha grabs you, you can do nothing but struggle to get free until Morpha throws you. If you land in the water, there are ladders on the four islands you can use to reach the surface again.
Morpha will eventually bring a second tentacle into the fight. This means you must be cautious as you wait for your opening to attack; listen to the sound effects to know if Morpha is getting ready to extend a tentacle, or if one is already extended. Keep suckering Morpha's tentacles out to grapple the cell and attack it until Morpha goes down for good. The water in the room will drain away, and you can jump into the dry pool to recover the Heart Container and step into the warp.

"Anyone who seeks fame need only become familiar with all that I have acheived." - Claudius Galen
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