There isn’t much to the Ancient Zora Waterworks, as it relies on one gimmick repeatedly. There are a bunch of rocks clogging up pipes, which you need to free by using either bomb flowers or hammer-like weapons. (Any weapon with a stone fused to it will work.)
Starting the Ancient Zora Waterworks
Once you get down there, you’ll notice the first clog directly ahead. Hit it with your rock weapon or bomb flower to open up the pipes, raising the water level. You’ll be able to proceed once the water rises up.
A chest will also float in the water, which you can grab and place on the ground to claim a Zora sword.
Continue on and you’ll be greeted with the main area and the actual text that says “Ancient Zora Waterworks” across your screen. You’ll need to fill up the room almost entirely in order to proceed.
Opening the first pipe
Starting at the bottom, the first clogged pipe will be on your left as you follow the broken bridge in front of you.
Use Ultrahand on the large wooden planks to give yourself some footing to break open the rocks.
Opening the second pipe
Once the rocks are broken and the water levels rise, turn towards the northeast to head to another broken bridge you can now access.
Head up the walkway, making sure to use Ultrahand on the wooden chest in the water on your left for a Zora shield.
Use the nearby large wooden planks to create a ramp that allows you to enter the hole in the wall. Break the rocks inside to raise the water level yet again.
Optional: fight an Ice Like and Bubbulfrog
Head to the new bridge you can now access in the northwest.
Head up the broken bridge, using Ultrahand on planks to climb up broken parts when necessary. At the end of the bridge, enter the cave on the right.
An enemy similar to the Sludge Like, called an Ice Like, will be inside, spitting clouds of ice at you. Between rounds of ice clouds, run up the slope past the Ice Like. The ice clouds will always travel towards the entrance of this cavern, so it’s best to be on high ground to kill it. If you don’t want to fight it, you can ignore it, but it’ll give you some materials and another Zora shield for your time.
At the end of the cave, there will be a Bubbulfrog, which you can take out for a Bubbul Gem. That’s it for this cavern and optional segment.
Opening the last pipe
Swim to the broken bridge in the west and enter the sewer-like pipe. There’ll be a few keese and chuchu inside, so take those out. If you keep following the pipes, it’ll spit you out on the other side of the waterworks near the optional Bubbulfrog cave mentioned above. However, you want to head towards the back of the pipe, where you can see water leaking through a grate.
Stand under the grate and use Ascend. Break the boulders directly in front of you to finish flooding the waterworks and climb up the ladder. Use Ultrahand on the lever to flip it to the other side.
Jump or glide down the opening and u-turn to enter a pipe with a chest inside. Open it for an opal.
Swim towards the lit up platform in the middle and interact with it. Link will chat a bit with Sidon, who will jump up the new waterfall spouting in the center of the lake.
Taking it will take you to the next part of the quest on Wellspring Island in the sky.
Before jumping in, make sure you have ample healing objects and splash fruit. You do not 100% need the latter in order to complete the upcoming island, but it’ll make your life significantly easier.