It was frozen due to a curse from Morpha, the monster Ganondorf sent to invade the Water Temple.
^ Both top answers are correct. Morpha cursed the Water Temple, which heavily affected the Ice Cavern in Lord Jabu Jabu's domain, the curse caused the Ice Cavern to blow icy bursts of wind. This likely caused Lord Jabu Jabu to retreat from Hyrule and migrate to Labrynna (not confirmed though). After Lord Jabu Jabu left, it caused Zora's Domain to become a frozen land, nearly void of life. Since fresh water from Zora's Domain flows into Lake Hylia, it caused the Lake to dry up almost completely. Timelinesplitter 23:03, June 6, 2012 (UTC)