Task 1: Getting the Clawshot
A Lever for Link
When you enter the temple, navigate through the watery passage until you hit dry land. Defeat the chus in the room, collecting whatever jellies you need, and head toward the gate. South of the ledge is a lever. Jump to it and grab onto it to make the gate open. You'll encounter many more levers as you proceed through the temple. You can also find a chest with a yellow rupee and a chest with water bombs in this room.
The Dungeon Map
In the next room, shoot the hanging stalactites with bomb arrows to create platforms. Head north across the chamber, and either fight or run from the helmasaurs (hit their vulnerable backside if you choose to fight). Go into the next room to the north.
In the large, circular room, you can rotate the central stairs by pulling levers. To reach the map, head downstairs and circle to the south of the room, then grab the lever to rotate the staircase. Afterwards, head back upstairs and grab the lever on the east side. Head down the stairs and go right to find the map.
Rise and Fall
Take the lower western exit out of the circular chamber and cross the bridge. In the next room, knock down the stalactites with bomb arrows, then head to the passage to the right. Climb around the central pillar using the vines and drop onto the western ledge. If you knocked down the most distant stalactite, the broken tip will form a platform on the geyser. Jump from the ledge to the stone pillar, and from there to the platform. Go to the chest and recover the small key nestled inside of it.
Return to the circular chamber and head upstairs. Circle around to the upper western door. You'll find Ooccoo on the door's left. Open the door with the small key and cross the bridge to the next chamber. Blast the stalactite near the northern wall to create a step that allows you to reach the vines and to climb to the top of the wall. From the wall's top, jump to and grab the lever, which opens a gate below you. Go down, continue through the chamber, and take the first door to the south.
A Spiraling Slope
You'll encounter a lizalfos in the round room where the giant cog is. After defeating it, take the southwest exit then head left to find a chest with a small key. Head back through the cog room and turn left. You'll encounter a boulder blocking your path. Destroy it with a bomb and continue into the next room, which contains a bubble enemy. Destroy its bubble with a bomb or bomb arrow, then attack the creature directly. Once it is defeated, use the small key to get through the locked door.
Head to the top of the western tower by taking the spiraling ramp. At the top you'll find an archway. Climb onto it and jump onto the lever to open the sluice and release the water. Ride down to the bottom of the room and swim to the large fish statue. Grab the lever there to open yet another sluice and follow the flowing water through the door. You'll end up back in the chamber where you found the small key. Enter the room with the huge cog inside and jump to the lower level and make your way to the east side. From there, jump to a moving platform and take the door leading north. Head left and grab a small key, then return to the moving platforms. Ride a platform to the western door. In the next room, use the small key to unlock the door to your left.
Miniboss: Deku Toad
Equip the iron boots and enter the water-filled passage. Avoiding the jellyfish, blow up the boulder with a water bomb to proceed through the passage, then swim up to the next chamber. Look at the ceiling like Midna suggests to begin a battle against an oversized frog. The toad drops down and the battle begins.
The Deku Toad sends a swarm of tadpoles after you. Use the spin attack to rid yourself of them. Once they are gone, the toad will leap into the air and try to squash you. Run away to avoid the attack, then hit its vulnerable tongue after it lands. Another way to damage the beast is to shoot a bomb arrow or throw a bomb into its open mouth, thereby causing it to collapse and its tongue to appear.
You will beat the toad after three rounds.It swings around, before spitting out a treasure chest. Collect your spoils: the clawshot.
Task 2: Finding the Boss
Another Watery Rush
Using the clawshot, target the red switch above the doorway to escape the room. Return to the central round room and head to the lower east side (use the clawshot to grapple the vines to get around the barriers). Hit the red switch with the clawshot, which will rotate the steps and allow water into the eastern chambers. Follow the flowing water through a door.
After entering the room that contains chained platforms and two giant cogs, grapple the gold and red target on the left side of the nearest cog. Drop to the pillar, get the bombs from the chest, and grapple to the vines on the northern wall. Grapple to the vines to climb the pillars, then grapple to the vines along the upper northern wall. Drop to the ledge and enter the door.
In the next chamber, use a bomb arrow to knock down the stalactite that's above the geyser, then ride the platform you've created to the top of the wall. Jump down and grapple to the ledge. In the next chamber, use the clawshot to grapple to the vines on the ceiling and bypass the barrier. Drop to the floor and ascend the tower. At the top, use the clawshot to grapple to the compass, then activate another lever.
To the Boss
The next goal is to reach the easternmost chambers on the first floor. The easiest way there is to return to the central room via the left passage from the east tower and re-enter the room containing the dual cogs on the first floor. Use the clawshot to latch onto the near cog and drop onto the pillar in the room's center. From there, grapple onto the second cog and drop off when you reach the eastern door.
Jump into the water and find a boulder near the middle of the area. Destroy it then go through the new passage and equip the iron boots to fall to the seafloor. Blow up another boulder in the southeast corner of the chamber. Proceed through the tunnel, then head to the surface and go through the door. Use the clawshot on the switch on the ceiling to open a hole in the floor. Lower yourself through the hole and receive the big key from the chest. Jump into the water and follow the underwater passage to make your exit.
Head back to the central chamber and jump into the water. Go to the central structure and open the door with the big key. Drop to the bottom of the chamber with the iron boots to enter the boss chamber.
Twilit Aquatic: Morpheel
Sink to the bottom of the large chamber. A tentacle is on the surface of the ground. Then the area around it rumbles, and Morpheel reveals itself.
The weak point of Morpheel is the eyeball inside its tentacle. Stay as far away from the boss as you can while staying in clawshot range, then grapple the eye out of the tentacle and hit it with your sword. If you get caught by a tentacle, unequip your iron boots and swim away before you get sucked into the boss's mouth.
After you pull out the eyeball a few times, Morpheel will emerge from its hole and start swimming around. Unequip your iron boots and start swimming. Position yourself above and behind the boss's head. When you are in range, target and grapple the eye on the back of Morpheel's head with the clawshot and then hit it repeatedly with your sword.
After several blows, Morpheel becomes blind. It swims around, not knowing where it's heading, and crashes into a wall. The water in the chamber drains, and the beast dies. You'll get a heart container and a fused shadow.