Step 1: Room A
This is the entrance to the temple, and where you can get a ride back to Zora Hall if you want. The first thing you need to do is take out your fire arrows, and light the four torches. A treasure chest appears. Open it and claim fairy #1. Now exit through the front door.
Step 2: Room B
Room B is pretty much the control center of the entire temple, mainly because this is where you control all of the water currents. Now change into Zora Link and swim to the yellow-green switch in the northeast corner of the room. Push it in a counterclockwise direction, and the knob disappears. Now, a jet has been turned on, allowing you to get to the next room. Go back to the door you entered, and you see platforms raising up and down. Before you take them to the next room, grab fairy #2 under the platform to the south, and fairy #3 by defeating the Giant Skultula on the southwest corner of the room. Now, take the rising platform to the left of the door you entered (when you face the door), defeat the Giant Skutulas, ride the water jet to get to the next platform, and exit through the northern exit.
Step 3: Room C
Room C is the main current center of the temple. You can remember this room by c for currents :) . This room will be seen often. In this room, grab fairy #4 in a barrel on the west side of the room (you have to climb up a ladder). Now to get fairy #5, it may take you a while. First, sink to the bottom near the center. DO NOT go into any of the openings yet! OK. Now use your bommerang attack to break the jar. Then grab the fairy. This is quite difficult to do, so try to keep your cool. Now exit the opening in the southeast corner with red and green tubes.
Step 4: Room D
Be careful when you come to the top of the water in this room. The water is inhabited by skull fish. Just fry them with your barrier attack. Swim to the lowest platform, and turn into normal Link when you get up there. Now use your Hookshot to get to the treasure chest to your right. Open it, and you get the Dungeon Map! Fairy #6 can be found in the jugs across from the treasure chest. Use your boomerang attack to break the jars, then turn into normal Link and put on the Great Fairy's Mask to attract it. Now, sink down and exit through the opening with red and green tubes that is guarded by dixiehands. Just swim through with your barrier attack on.
Step 5: Room E
As you enter this room, you see that it is home to four Bio Deku Babas. Use the boomerang attack at their bodies, and they will die. If you hit it at it's stem, it will fall down, and you have to face it on ground. Destroy the ones on the lily pads, and kill the one in the little alcove. Once you've killed them all, a treasure chest appears across from the lily pads. Jump across them, open the chest, and claim fairy #7. Exit through the door infront of you.
Step 6: Room F
This room is different. You come in and you see a bombchu roaming around. Shoot it with your bow to make things safer. Now, jump in the water and sink down. Destroy the dixiehand and grab they small key from the chest. Now come back up to the water and jump across the lily pads to the treasure chest. Open it and you get the Compass. Now to get fairy #8, go to the platform near where you entered. You should see two dixiehands guarding a clay pot. destroy the dixehands by using your boomerang attack, and break the clay pot. Now return to normal Link, and wear the great fairy's mask to get the fairy. Now jump into the water, and you head back to Room C. Enter the opening with the red tube at the very bottom.
Step 7: Room G
Simply raise to the surface, walk across the red pipe watching out for the bombchu, and enter the locked door.
Step 8: Rooms H&I
Room H is more like a hallway to collect arrows. Arrows will be very helpful in the next room, so be sure to be full on your arrows. Collect them from all of the jars and the chuchus in the room. Enter Room I and you get locked in. There seems to be no movement anywhere until you look up at the ceiling. Now, a big eyeball falls down from the ceiling and bubbles surround him as he is ready for combat. This is Wart, the temple's first Miniboss. He is pretty tough to defeat, and may take a while. First, you can use your bow to knock down the bubbles, but I find that to be a waste. What I do, is run up to Wart and start slashing him like crazy! This will knock down a lot of bubbles. Destroy them all with a slash of your sword. Now, when Wart opens his eye, shoot him with an arrow. Make sure to shoot the eye, and not a bubble. If bubbles are still in the way, go ahead and destroy them. Now, shoot Wart in the eye three times, and he goes into a frenzy. Slash him with your sword when he is coming at you with is eye open and the battle is done. This is pretty tough to do. Once you beat him, a treasure chest appears, and you get the Ice Arrows. Use these to freeze things and use them as stepping stones. Now head back through Room H into Room G.
Step 9: Room G
Now, head over to the platform on the opposite side of Room H. Now shoot the octoroks with the ice arrows, and jump onto the platform with the knob. Turn it, and head back to Room C. Head back to Room D (the one with red and green tubes in the southeast corner), and use the Ice Arrowsto make platforms in the water to get to the door on the other side.
Step 10: Room J
Inside this room is a blue chuchu. Shoot it with the ice arrows and push it towards the red valve platform. Use him as a climbing block. Get on the plaform, and turn the valve. Now, go back to Room D, and take the tube to Room F. Use the ice arrows and lily pads to get across to the room next to the boss key. Destroy the stalactites, collect the arrows in them, and enter the room.
Step 11: Room K
When you enter, it's time to fight another Gekko. This time, he fights a bit different. First, he has Mad Jellies surrounding him. When he jumps up to the ceiling, the surround him. Here, you shoot ice arrows at the jelly on the ceiling. You have a pretty short time to do so, so do it fast. Then run away to let the ice fall, then run towards the Gekko and slash him as many times as you can. If you miss the jelly, the Gekko pulls you into the mess and beats you up. I am pretty sure that you can destroy some of the Mad Jellies, but not all of them. Once you've beaten the Gekko, step into the room that just opened, and you get the Boss Key!