Link remembered Sheik mentioning a temple of water. Navi felt an artic wind blowing from Zora's River, so Link traveled up Zora's River to the entrance of Zora's Domain. It was indeed cold, and, strangely enough, Link could see snowflakes in the air. He entered Zora's Domain and stood frozen in shock. The entire domain was a tomb of ice. It appeared that all of the water had frozen at once, trapping helpless Zoras inside of it. Even King Zora was frozen in enchanted red ice.
Lord Jabu-Jabu was gone from Zora's Fountain, and ice floes floated in the icy cold water. Link jumped from glacier to glacier and found a cave in the mountainside. The cave was filled with ice and strange icy enemies. While exploring inside Link defeated a White Wolfos. Suddenly, Sheik appeared out of nowhere.
If you came here to meet the Zoras, you wasted your time. This is all there is. With one exception, the Zoras are all now sealed under this thick ice sheet. I managed to rescue the Zora princess from under the ice, but she left to head for the Water Temple. This ice is created by an evil curse. The monster in the Water Temple is the source of the curse. Unless you shut off the source, this ice will never melt.
Sheik taught Link the Serenade of Water to lead him to the Water Temple, and disappeared in a flash of light. Inside the treasure chest in that room Link picked up a pair of Iron Boots, which could be used to sink in water and walk on the bottom. Catching some blue fire in a bottle, Link headed back to Zora's Domain. The blue fire freed King Zora from his icy imprisonment, and the King awarded Link with the Zora Tunic, which enabled him to breathe underwater. Link told him that Ruto was in the Water Temple, and then headed after her.
Putting the Ocarina of Time to his lips, Link played the Serenade of Water, and was transported to an island in the middle of Lake Hylia. This lake had once been a large expanse of water, but now the reduced flow of water from Zora's Fountain had sunk the lake to a much lower level. Using the Iron Boots, Link sank to the bottom of what was left of the lake, and entered the Water Temple.
Link explored the bottom of the water-filled temple, and found his "finacée," Princess Ruto of the Zoras. She had never forgotten their vows, and jokingly scolded him for keeping her waiting for seven long years. As the woman who would be his wife, she requested that Link help her destroy the evil monster in the Temple, and told him to follow her to a place where he could change the level of the Temple's water. Link followed her to the surface, but he lost sight of her and couldn't find her again.
Link wandered through the Temple, changing the water level and making good use of the Iron Boots. He came to an outdoor area filled with fog and highly reflective water, an odd change of surroundings from the rest of the Temple. Suddenly, next to a tree appeared what looked like Link. It was Shadow Link, and evil replica of the hero, and it mirrored his every move. Link tried to outsmart it and catch it by surprise, but it blocked his every move. Finally, he was forced to use magic, and cast Din's Fire to defeat his powerful double. With the defeat of the Shadow, the deceit of Link's surroundings melted away, revealing just another room in the Water Temple. Through a door at the end of the hall Link opened a treasure chest, which contained the Longshot, a longer-range hookshot.
After more searching, Link at last found the source of the curse on Zora's Domain. The giant aquatic amoeba, Morpha, who had complete control of water, rose from a pool of abnormal water and tried to grab Link and pull him under. Link defeated the morphing, oozing water monster by pulling out its innerds with the Longshot and acquainting it with the might of his blade. When the evil monster destroyed, the abnormal water, along with the curse on Zora's Domain, evaporated into nothing.
Link was transported to the Chamber of Sages to witness Princess Ruto's awakening as the Sage of Water. She said that Zora's Domain and her people would eventually return to their original state. She would have liked to reward him with her eternal love, but instead she encouraged him on his quest for justice and peace, and gave him the Water Medallion.
Link warped to Lake Hylia, which, with the disappearing evil, was filling up fast to its original level. Sheik was there watching, and he congratulated Link on his and Ruto's victory. Link looked out at the peace and purity that had returned to the lake, and when he turned around again Sheik was gone. He was on top of a tall tree trunk, and he dove into the water and disappeared before Link could say good-bye.
Link noticed a stone monolith set up nearby, and read the inscription:
When water fills the lake,
shoot for the morning light.
The sun was rising just then, so Link pulled out his Fairy Bow and shot an arrow at the sun. The arrow was engulfed in flame, and slowly sank back down to earth onto an island in the lake. Link swam out to the island and picked up the magical Fire Arrows, which he could now shoot his enemies.