How to Refill Hylia in Ocarina of Time

Finish the Ice Cavern quest to obtain the Iron Boots. You will need them to access the Water Temple under Lake Hylia. Play the "Serenade of Water" to warp to Lake Hylia once you have them.

Go to the Lakeside Laboratory and use the boots to sink to the bottom of the pool inside. Continue all the way to the bottom until you see a gate with a glowing blue crystal above. Shoot the crystal with your slingshot. The gate will open. This is the entrance to the Water Temple.

Enter the gate and make your way through the Water Temple. You will come to a room that is not flooded and contains a pool with four platforms arranged in a square in the middle. Jump onto one of the platforms. A cutscene will play, after which you will be attacked by Morpha, the Water Temple boss.

Defeat Morpha. Morpha is a tentacle of water with a brain floating inside. It attacks by striking at you with further tentacles it generates from the surrounding pool. Dodge these as best you can and use the Longshot to target and harness the brain. Draw it near and attack it with your sword. If Morpha manages to hit you, the Longshot will lose its grip and you will have to harness its brain again. Continue doing this until the brain explodes. Morpha will die and a cutscene will play.

Return to the surface by using the blue warp portal that appears at the bottom of the pool. A long cutscene will play in which a number of important plot elements are revealed. At the end of the cut scene, Lake Hylia will refill.