Zora's Fountain

Zora's Fountain is the source of all of Hyrule's water, in Ocarina of Time. The Zora's Fountain is connected to Zora's Domain and Zora's River. At the back of the fountain is the Ice Cavern and a Fairy Fountain. Floating in the center of the fountain is Lord Jabu Jabu. It is also very deep. If the Link sinks to the bottom with the Zora Tunic and Iron Boots, he will find a Heart Piece and several green rupees.

Theoretical Connection & Explanation
Zora's Fountain was not "present" in Twilight Princess as its own separate area from Zora's Domain, but instead, the throne room was. The easiest understanding of where Zora's Fountain went is that the developers redesigned it so that it became the immense, deep pool in the throne room - with a nice spring right at the bottom, hence the name "Zora's Fountain".

In Ocarina of Time, Zora's Fountain ended in a giant waterfall, feeding Zora's River. Through the geographically morphed design of Twilight Princess, Zora's Fountain became part of the infrastructure of Zora's Domain and helped to balance the entire area and create the enormous waterfall that is seen in the new Zora's Domain.

Lord Jabu-Jabu has unfortunately remained missing as he was in Link's adulthood of Ocarina of Time.