Found this online, this should help:
When you arrive here, equip the Zora Tunic and then float up to the surface with the Kokiri Boots. When you surface, get onto the nearby platform and then use the Hookshot on the black and white target to the north, on the building there. Now, when you reach the building, equip the Iron Boots and sink underwater until you are underneath the building. When you are, take the nearby right tunnel and follow it, into the next room. In that room, you'll meet Princess Ruto again! She will talk for a minute, then float up to the area above.
When you regain control, switch to the Kokiri Boots and follow Ruto up there. When you reach the surface, climb into the room and then use Din's Fire to light all of the torches in the room. After that, the door will open, so enter it, into the next area. In this area, defeat the three Stalfos enemies. When they are defeated, use the Hookshot on the panel on the wall. When you do, a chest will spawn, which contains a Dungeon Map. A Fairy will also spawn, so capture it in a bottle. Open the chest for the Dungeon Map, then exit this room. In the previous room, play Zelda's Lullaby beside the Triforce symbol on the wall, as when you do this, the water will drain. When the water drains, drop down to the area where you met Ruto.
Once there, use Din's Fire to light all of the unlit torches in the room. When the torches are lit, the door opens, so enter it, into the next room. In this next room, defeat the Spike enemy and the Lizalfos enemies. When they are defeated, a chest will spawn, so open it for a Compass. Now, exit the room, back into the previous area we go. In the previous room, Hookshot to one of the black pillars that have the black and white targets on them.
When you are on top of one, look up and then when you see the black and white target, Hookshot to it. Then, climb on top of the black and white target and go into the next room. In this room, use the Hookshot on the panel on the wall to make a chest appear. This chest contains the Longshot! Like I said, this dungeon is MUCH easier than the one in Ocarina of Time, thank God.
Once you have the Longshot, drop back down to the area below, and then go out of the tunnel, back into the once underwater area. Back in that area, Longshot to the black and white target on the tower (The building in the center of the room.). When you are on the tower, enter the door, into the next area. In this area, jump to the platform with the Triforce symbol on the wall below you. On that platform, play Zelda's Lullaby beside the Triforce symbol to raise the water level to mid-level. When the water in the temple is raised to mid-level, exit this room via the way you came.
Back in the previous area on the tower, dive into the water and climb up on the platform with the black and white targets. Once there, use the Longshot on the black and white target directly above you on the tower to reach the third floor. When you reach the third floor of the temple, walk across the tower until you see an alcove with a Triforce symbol. When you do, Longshot to the black and white target in the alcove. In the alcove, play Zelda's Lullaby beside the Triforce symbol to raise the water level to its maximum heighth. When the water is raised, equip the Iron Boots and get in the water and then make your way back into the door that you raised the water to mid-level in (Or, tower, if you prefer.).
In that room, equip the Kokiri Boots and float up to the surface. When you surface, stand on the highest platform in the room, then Navi will turn green. When she does, play the Song of Time to make a Time Block appear. Jump up onto the Time Block, then stand in the middle of the Time Block and use Din's Fire to light the torches in the room. When the torches are lit, equip the Iron Boots and then drop down into the water. When you reach the area with spikes, drop down into the hole there, into the next room. In this room, ignore every obstacle and keep following the path in the room until you come across two brown stairs. When you do, stand on the upper one and they will both collapse, and a crystal switch is revealed.
Hit this crystal switch with your Longshot. Once you hit the crystal switch, go north, then turn east and look up; you should see the opening that you just opened after hitting the crystal switch. When you see it, Longshot to the black and white target in the room above you. In that room, Longshot the panel on the wall and a Magic Jar, as well as a chest spawns. Open the chest for a Small Key. Once you have that, head back to the area below, then all the way back up to the main room (The room with the tower.). Back in that room, surface up and jump on the platform with the locked door. Unlock it. In this next room, drop down onto the platform below you, but be careful not to fall off.
When you are on the platform, look left and up and you should see a crystal switch. When you do, shoot it. Now, this part is a bit tricky. This is really actually the only hard part in the Water Temple in MQ. What you have to do is use the Longshot on the black and white target directly above the leftmost one. If done successfully, you'll be on the black and white target below the uppermost one on the left side of the waterfall. On that target, look up and then Longshot to the highest black and white target on the waterfall, then you'll drop down to another black and white target. On that one, look up and then to the left and you should see a panel on the wall. When you see it, shoot it with your Longshot.
Doing this will cause a Fairy to come out, and also make the black pillar that has the black and white target at the very top of the waterfall to rise up. Longshot to the black and white target up at the top of the waterfall, then jump onto the platform and enter the door into the next room. In this room, drop down into the water and kill the three Stalfos enemies that immediately attack you. When they are dead, Longshot to the dragon statue with the black and white target to your right. Then, move south on the platform a bit, then look up and you should see another dragon statue with a black and white target on it. Longshot to that when you see it. On this platform, head north and look up and you should see another black and white target, but not on a statue, it is on the ceiling instead.
Longshot to it. Then, go through the door, into the next area. Before you go, though, break the two jars, as they house Magic Jars, which you will need in the next room. Anyway, in this next room, head north to the door at the other end of the room. Then, head north again like you are going back to the other door, and you'll see a shadow of yourself beside the tree. This is Dark Link, the mini-boss of the Water Temple. This is a VERY hard mini-boss, mind you, so I hope you have at least one Fairy, as this guy is no push over.
Dark Link can copy every one of your moves that you do, except for Din's Fire. Even with a full upgraded Magic Meter from Death Mountain Crater, you cannot defeat Dark Link if you used all your magic up on Din's Fire. With that said, be very careful when fighting this guy. After Dark Link is defeated, the room's design will change and look more like the Water Temple, so head through the nearby door, into the next area. In this area, break the two jars on the platform to get a Fairy and a random item. Now, Longshot the panel on the wall and the gate below it will open, thus giving you access further into the dungeon. Head down the hole. In this next area, you're in a watery area with vortexes.
Longshot to the black pillar with the black and white target in the water. Once you Longshot to that, keep using the Longshot on the other pillars with the black and white targets on them until you reach an area where there is no other pillars. When you reach that point in the room, look up and then you should see a black and white target. Longshot to it. Once you are on the small side ledge in the water, Longshot to the black and white target just to the north of you, on the wall above the side ledge in front of you. Once you are on that side ledge, Longshot to the black pillar with the black and white target in the water, then jump to the platform in front of you. Now, follow the path into a new watery room. When you reach this room, equip the Iron Boots and drop down into the water. In the water, look across the room until you spot a black and white target, as well as some wooden crates.
When you spot this, Longshot to the black and white target. Then, in this alcove, ignore the crates and look up; you should see a black and white target on the ceiling in another room, so Longshot to it when you see it. In this next room, use Din's Fire to light the torches in the room. When the torches are lit, head back to the previous room. In the previous room, equip the Kokiri Boots again and float back up to the surface. On the surface, get yourself onto the ledge with the wooden crates, then enter the door into the next room. In this room, hit the nearby crystal switch to cause a pillar of water to come from the floor. When it does so, get on top of it and ride it up as far as it can go. Then, use Din's Fire to light the torches in the gated area to your north.
Once the torches are lit, the gates will open, so Longshot to the black and white target then open the yellow and blue chest there for the Boss Key of the dungeon! Once you have the Boss Key, head north and then jump into the pit of water, then switch to the Iron Boots once more. Then, switch to the Kokiri Boots and float up to the area above. In this area, put the Iron Boots back on yet again, then step on the switch to open the nearby gate. Head through the area that the gate was blocking, and it happens to be the main room of the temple! Switch to the Kokiri Boots once last time, then Longshot to the black and white target on the dragon statue in the room. Once you Longshot there, head through the door into the next area.
In this area, look above the boss door and shoot the crystal switch with your Longshot. This will cause black pillars with black and white targets to rise in the room, so Longshot over to one of them beside the boss door. Then, when you reach the other side, enter the door into the boss room. In that room, jump into the weird water, then climb up onto one of the platforms in the water. Then, the boss of this dungeon, Morpha will come out and attack you!
Defeating Morpha is rather easy, actually. The way to beat him is to head into a corner. When you are in the corner, Morpha cannot hurt you! Anyway, to attack Morpha, wait until the nucleus thing comes out close enough, so that you can Longshot it. When it does so, use the Longshot to launch the nucleus over to you. When it is over to where you are, strike it with your sword. Morpha will do the same thing over and over, so repeat until you've won. Also, something I forgot to mention, is that there will eventually be two Morphas; one that contains the nucleus, and one that does not. NOTE: Something else I forgot to mention, is when you are in a corner, Morpha will just stay there, and you won't be able to hit the nucleus. When this happens, run across to another side of the room, and along the way, try and hit the nucleus.
When Morpha is defeated, grab the Heart Container in the pit that is no longer underwater, save your game, and enter the blue portal. You will be warped to the Chamber of the Sages.
it was the water level -__-