Zora's Fountain

Zora's Fountain is the source of all of Hyrule's water in Ocarina of Time, and it is connected to Zora's Domain and Zora's River. Located at the back of the fountain is the Ice Cavern and a Fairy Fountain, while resting in the center is Lord Jabu-Jabu. This is also the place where Link ultimately receives the Zora's Sapphire from Princess Ruto.

If Link sinks to the bottom with the Zora Tunic and Iron Boots, he will find a Heart Piece and several green rupees. Likewise, when he finds the Silver Gauntlets in the Spirit Temple, he can lift a stone near the Great Fairy's Fountain to discover an underground passage; using the Lens of Truth, he can see and defeat invisible enemies within, then explore the passage to climb towards the hideout of a Gold Skulltula.

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 the Sleepless Waterfall, 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 in Twilight Princess as he was in Link's adulthood of Ocarina of Time.