The water bubble will protect Link from one attack if he’s hit. More importantly, though, attacking while the bubble is in effect will shoot the bubble as a watery projectile.
The projectile varies based on your weapon type, as well, with spears having the fastest projectile.
Avoid Mucktorok’s muck shark attacks while waiting for Sidon to charge his ability, then approach him and get the Water Bubble. Wait for an opening and press A to shoot the water projectile at the shark.
The water will dissolve the shark with a single hit, leaving Mucktorok exposed. It’s your chance to go on the offensive, so grab your strongest weapon and beat Mucktorok up while you can!
Phase 2 will start once the boss’ health is below 50%! There are only two big differences for this phase.
First, Mucktorok will cover most of the arena with muck. Link won’t take damage by standing on it, but he will be slowed down greatly. Your Water Bubble projectiles can remove the sludge.
Second, Mucktorok will be able to swim through the muck after being exposed. This makes it much harder to catch.
Other than that, the fight remains mostly the same: avoid the shark’s attacks, get Sidon’s Water Bubble, and expose the boss to be able to deal damage.
Repeat the process until you empty the boss’ health bar and you will have won, completing the Water Temple!