There are two storyline arguments I usually go by:
1: Split Timeline Theory: This occurs during OoT. When the game ends, the story supposedly splits into two separate timelines, Adult and Child. What you said is known as the Child Timeline, where Link defeats Ganon and then goes back to the past in the Temple of Time, and he and Zelda somehow convince the King not to trust Ganondorf (I'm fuzzy on the details... >_>) and Link heads off to Termina to start the events of Majora's Mask, which subsequently leads into Wind Waker/PH/ST. The other timeline is the Adult Timeline, where Link remains an adult after defeating Ganon and Hyrule is rebuilt. This timeline leads to Twilight Princess, so either Zora's Domain was never unfrozen in all that time or it was and it was re-unfrozen when Ganondorf came back with Zant in the beginning of TP.
2: No Timeline: There is not a timeline beyond direct sequels (i.e. the DS ones) and each game is separate unto itself. But where's the fun there? ;D