Instructions
Acquire the fairy bow from the Forest Temple, the iron boots from the Ice Cavern and the Zora's tunic from the Zora's Domain shop before attempting to play through the Water Temple. All of these items are required to get the boss key in the Water Temple.
Explore the temple as thoroughly as possible. If you get stuck, search for any switches to hit with an arrow, the hookshot or the longshot, as well as any blocks to push or pull, any torches to light, any targets that can be grabbed by the hookshot or longshot, any cracks that can be bombed and any holes in the ceiling. You can manipulate the level of the water in the temple at multiple places, so if you see a hole in the roof, raise the water level, remove the iron boots and float up through the hole in the roof.
Find all six small keys in the temple. All of these keys are required to enter the room containing the boss key. Three of these keys are located on the first floor, two are located on the second floor and one is located in the basement. In order to get most of these keys, you will need to solve a few small puzzles. Pay special attention to your surroundings to help you figure out these puzzles.
Raise the water up to the first floor level once you have acquired all six keys, most of which you will have used by now. Enter the boulder channel on the first floor, and equip the iron boots.
Jump toward the source of the boulders immediately after one passes. Follow the underwater passage until you reach the end. Remove the iron boots and float to the surface. Unlock the door and enter the next room. The boss key is contained in a blue treasure chest in this room.