There are two different Wells of Eternity. There is the original Well of Eternity (or the First Well of Eternity) that stood before and during the War of the Ancients, and once it collapsed on itself blasted the supercontinent Kalimdor apart in what is called the Great Sundering, which was a lake crafted by the titans that contained immense energy. The present area where the original Well of Eternity was is now the Maelstrom in the center of what is now the Great Sea.
The second Well of Eternity - or the Second Well of Eternity - was created by Illidan Stormrage using three of seven vials of water - from the original Well of Eternity that he collected before it collapsed on itself - and pouring them into a lake he found atop Mount Hyjal. It was quickly covered by Nordrassil, the original World Tree.