The Great Bay Temple is a mechanical construct meant to control the Ocean's temperature. It's currently warmer than usual, which is unhealthy to the Zora eggs in the Ocean, and needs to be resolved.
The first room you will see is the waterwheel room. To get through the room, you need to turn on the yellow switch located under the water. This enables a water jet that you can use when you ride the eastern lift to the top.
The next room is the turbine room, which spins either clockwise or counterclockwise depending on the turn of the waterwheel. First, enter the south-east exit, and collect the map from the chest.
Enter the south-east tunnel, and reach the next room to collect the key. YOu may optionally get the compass as well from the same room. Enter the fast-moving water stream to return to the turbine.
Next, move to the north-west exit, and walk onto the red pipe exiting to the North. Collect as much magic power and arrows as you can to defeat the Wart. You first need to clear out the bubbles surrounding it with fire arrows, then hit it's eye when it's open. When it's low on health, it will release its protection, and begin to zip wildly around the room, but it still vulnerable to eye shots when it is open. If you need a safe area in the latter part of the fight, stand in one of the corners; you can also use the shield to block the fast moving attack.
Once defeated, you can get Ice Arrows, and freeze the octopods to the south. Climb to the central valve and turn it. Head to the south-east room again, and use ice arrows to build a path to the south door. Freeze the Blue Chuchu and climb to the red valve and open it. Return to the entrance room, hookshot the ceiling above the red water spout and turn the valve. This will stop the wheel; close the yellow valve to restart it.
Head to the north, and freeze the water flow blocking access to the ladder, Enter and use ice arrows to reach the green valve to open it.
Head north east from the turbine room, and surface to enter the first room. Freeze the floor to that room, and melt the ice on the door with a fire arrow. You will now fight a Mad Jelly and its Gekko assistant; to kill it, use Ice Arrows on both the frog and large jelly. It should not take more than 10 hits; on a successful blow, the frog either forms the jelly in a large blob, or your ice arrow breaks the jelly into small bits. Once defeated, you can exit to get the boss key.
Continue along the water route. Head up the lefts on the west, and jump onto the second lift. Freeze the ice channel above, and walk across the wheel to the next room.
Within the see-saw rooms, you need to stand on one side of the see-saw and either freeze or melt the water channels above. Go the far see-saw first, and use the two see-saws to reach and open the green valve. Head to the first one to return to the chamber south-west of the turbine.
Return to the turbine, and take the south exit. Open the final valve and enter the boss room,
Gyorg is a large pirhana. It will ram the platform you are standing on if you stand near the edge. If you are standing in the middle when it is beginning its charge, it will jump over the platform, knocking you down. It will chase you if you are in the water and will drag you around if it catches you, hurting you in the process.
Shoot an arrow at it's head to stun it. While it's stunned, dive and use the electrified ram (R) to damage it. It will not stay stunned for long, so it is best to stun it while it is near the platform. This process will require changing your mask a lot.
When it is damaged, it will release little piranhas into the water. While the pirahnas do damage when they attack, when destroyed they will each give you a heart. Continue fighting the same way, but avoid the little pirahnas when in the water.
After Gyorg is damaged for the last time, it will flop onto the platform and leave a heart piece and its mask. Be sure to grab the heart piece first.
When you have all fifteen, return to Zora Cape and leap from the rocks to the south and use the hookshot to travel to the rest of the stray rocks. Blast the boulders with the bomb, and head inside to the fountain.
The Great Fairy of Courage will strengthen your defence, causing them to inflict only half as much damage.