Under the East Reservoir Lake at the pillar of light, you discover the Ancient Zora Waterworks.
The Ancient Zora Waterworks is located at 3603, 0128, 0202, in the whirlpool in East Reservoir Lake, southeast of Zora's Domain. It can only be entered after you complete the main quest Clues to the Sky and defeat the Sludge Like, then go south to the quest location and talk to Sidon, who will open the way to the cave.
Break the Boulders
In the first area of the Ancient Zora Waterworks, there is a boulder blocking a water spout to the east. Destroy the boulder.
The path will lead you to the main area of the Ancient Zora Waterworks. West of where you entered the room, there is another boulder. Destroy it to raise the water.
Now you can go to the east side of the room to reach a ramp to a pipe in the wall. Attach the three narrow boards together, then lean them up against the pipe opening to make a ramp that you can walk up. Go into the pipe and destroy the boulders that are blocking the water.
Now go north to a ramp that you can now reach. If you go east when you reach the wall, and keep going along the stone ledge, you will find a well-hidden tunnel that leads to an Ice Like, and beyond that, you will find this cave's Bubbulfrog.
Exit the Bubbulfrog tunnel and go west along the north wall, and you will find a large pipe in the wall. There is also a smaller pipe farther down from the large one. Glide into the smaller pipe, or place a wooden board under it and use Ascend to enter it.
Go through the side tunnels until you reach a room to the northwest that has water pouring down from above. Use Ascend here to reach the area where boulders are blocking the water. Break the boulders to raise the water level.
To leave this room, go up the ladder against the wall. At the end of the path, flip the switch to open the bars. Then glide down to the south side of the glowing building. Check on the glowing object there. There will be a cutscene. Use the Zora Armor to swim up the waterfall, and you will arrive on Wellspring Island.
After the Water Temple
After you complete the Water Temple, you can come back to the Ancient Zora Waterworks to find that the water has drained away. Go to the northern part of the area, at 3664, 0334, -0049, to find a hole in the ground that wasn't reachable before. Go down the hole.
In the middle of this area, there is a Stone Talus (Luminous).
Go southwest from there to find a waterfall with a lamp behind it. Go into the tunnel behind the waterfall to find a chest that contains the Zora Greaves.