Instructions
Enter the Gerudo Training Ground in the Gerudo Fortress. You can not access the Fortress until you complete your first visit to the Spirit Temple and obtain the Gerudo's Membership card. Do the Gerudo Training Ground side quest right after your first visit to the Spirit Temple, so you get the most out of the ice arrows.
Enter the Water Room. You'll see time blocks after you solve the puzzle in the Lava Room. Pull out your ocarina and play the Song of Time to remove these blocks and reveal a pool of water.
Jump into the pool of water. Link will float at the top. Equip the Zora Tunic to enable Link to breathe underwater. Then, equip the Iron Boots and sink to the bottom of the water.
Walk to the center of the room and collect the silver rupee. You may have to destroy the Shell Blades with your Longshot weapon in order to safely access the area.
Locate the next silver rupee in one corner of the room. It is slightly above Link's head and out of his reach while he wears the Iron Boots. Stand below the rupee and remove the Iron Boots. Link will collect the rupee as he floats upward.
Float all the way to the ceiling and swim around all four sides of the room. You will see a silver rupee as you swim around. Swim into it and you'll automatically collect it.
Put the Iron Boots back on and sink to the bottom of the room. Walk to one side of the room and stand below the silver rupee with a target above it. Pull out your Longshot weapon and aim it at the target. When you hit the target, you'll be pulled upward. Link will automatically grab the silver rupee along the way.
Walk along the bottom of the room with the Iron Boots. You will see one more rupee that floats above Link. Stand so that Link, the rupee and a target on the wall form a diagonal line. Use the Longshot on the target. Link will pull himself upward and collect the rupee. You'll see a cut scene in which a treasure chest appears in another room. Remove the Iron Boots and swim to the center of the room to float up to the surface.