Divine Beast Vah Ruta is a large Elephant like machine that is located in the lake near the Zora Domain. The beast is generating a disturbance by causing a constant rainfall that is threatening to flood Hyrule. It is a fairly easy dungeon with a tricky enough boss fight at the end. See below for the full Vah Ruta walkthrough including the puzzle and boss fight walkthrough.
Stage 1 - Water Battle
The first part of this comes in the form of a battle on the lake. You will need to use the shock arrows that you recently acquired to shoot the red orbs on the shoulders of Vah Ruta. The Zora prince will be bringing you around the water, so you have no need to worry about the navigation. You need to focus on 2 things, the ice blocks and shooting the red orbs.
When you are near the waterfall ( with the Zora armor equipped ), you will be able to swim up the waterfall near Vah Ruta's shoulder by pressing A. Do this and link will fly up in the air. Press the trigger button and shoot the red orb with a shock arrow. You need to repeat this process for the remaining 3 orbs.
After hitting 1 orb, you will then have to defend yourself against the attacks. Large ice blocks will be shot at you. Use the ice rune to shatter the blocks before they hit you.
Step 2 - Vah Ruta Walkthrough
This is the main puzzle of this dungeon and is quite a fun, yet tricky one to solve. There is very little combat here, but you should still be well equipped as there is a tough boss fight.
Terminal 1 - From the point where you start, walk into the main room and turn to the left. Cast an ice block on the water that is underneath the iron gate to lift it up. Activate the terminal inside.
Terminal 2 - From the location of Terminal 1, turn around and walk to the other side of the room. There will be a door that leads down into a larger room. To the left of this doorway is a gear on the wall. Use the magnetic rune to spin this gear and it will lift up another terminal.
Terminal 3 - After interacting with terminal 2, turn around and head out the door on the right. After making your way up, you will see a spinning gear that is being pushed by water. If you look inside the wheel, there is a terminal that is spinning inside. You will need to cast an ice block at the water source to stop the wheel from spinning. You need to time this correctly so that the terminal isn't upside down when you stop the wheel from spinning.
Terminal 4 - The next terminal is inside the larger wheel in the middle of the room. Directly across from the door which you entered is another door. Walk through this. There will be a demon mouth thing in the way. On the upper left side of the wall is an eye that you can shoot to destroy it all. Make your way up to the point where you are standing on the platform at the center of the large wheel. The wheel won't be spinning at the moment. If you view the map, you will see that you are able to control the trunk of the elephant. Move this trunk upwards and the water will shoot over its back and begin turning the wheel in an anti-clockwise direction.
If you look you will see there is a ball that will activate the door to the terminal, but it falls out before you can get into it. You will need to use the freeze time rune, to freeze the ball before it falls out. This will give you time to get to the terminal before it falls out.
Terminal 5 - Head back to the wheel that you used to unlock terminal 3. Now that the large wheel is spinning, you can jump on it and it will take you to the other side. Straight ahead if you is a corridor with a wall at the end. Walk to the end of this and then alter the elephant's trunk in the map menu so it is extended fully forward. Walk as far forward as you possibly can. Glide over to the very tip of the trunk and stand near the part that is spouting the water. There is a terminal on the part of the trunk that is pointing at the ground. Lift the trunk upwards again and walk with the movement so you can get to the terminal at the tip of the trunk.
Terminal 6 - You should be standing at terminal 5 at the tip of Vah Ruta's trunk. Make the trunk fully curl up so that you can see over the head of the elephant. Glide over and land on the elephants head. There will be a small hole here that you can jump down through. You will see the terminal surrounded in flames. Above the terminal is a platform with a gear. Use the same method used from Terminal 2 to spin the gear. This will open up the roof above the terminal. Move the trunk again so that the water spills in and puts out the fire (assuming it didn't happen when you opened it up. Go and get the terminal and that's it! Make your way down to the main computer to begin the boss battle.
Stage 3 - Waterblight Gannon Boss Fight
To my surprise, this turned out to be a fairly tricky boss fight, at least for Zelda standards. However, it's not all that bad once you know the right approach to take. There are 2 stages to this fight, the methods of dealing damage will remain the same for both. A shield is of little use in this fight, so no need to worry about having a good one. I would suggest using a good spear, but a sword will do too. You will also need to have some arrows to stun the boss. They don't need to be any particular type, but the elemental arrows do deal more damage.
Start by dodging his attacks. He does little to defend himself as he is full on offensive. So long as you dodge, you will be able to do plenty of damage this way, but using arrows is the best. From a distance, shoot an arrow at his eye. It takes 2 standard arrows to stun him. When he falls to the ground, head over and hit him with everything you got. After you take away about 50% of his health the second stage will start. The room will fill with water and you will be restricted to 4 small platforms. Use the ice rune to destroy the ice blocks he fires at you, just like stage 1 of Vah Ruta. Shoot him in the eye with more arrows and when he falls make your way over to him and deal some damage. The closer you are to him the better as swimming is slow. Keep repeating this process until he is dead.
This video guide for killing Waterblight Gannon may help if you are still stuck with this boss fight.
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