9.1 Strike Down the Lizalfos!
From the entrance, swim through the passage until you reach the surface. The Treasure Chests here contain 20 Arrows and 10 Water Bombs, in case you have run out of them. With your back to the door, jump and grab hold of the switch hanging from the ceiling. This unlocks the door to the next room.
In the second room there are many stalactites hanging from the ceiling. Knock them down with Bomb Arrows and climb on them to reach the door.
Go through the third room and enter the Temple’s main room. Go down the stairs in front of you then go right halfway around the room. Pull the switch here to re-position the staircase. Go up the stairs and go right a quarter of the way around the room to find another switch: pull it and go downstairs again. The Treasure Chest on your right contains the Dungeon Map. Open the door and cross the bridge to the next room.
9.2 The First Floodgate
Take the path that slopes downward on your right. Shoot down a stalactite with a Bomb Arrow to plug the gap. Climb along the vines to your right and shoot down another stalactite to create a platform. Use this to reach the Treasure Chest on the high ledge; it contains a Small Key. Go back to the entrance.
Return to the main room and go up the stairs. Go left halfway around the room and open the locked door with the Small Key. Cross the bridge and enter the next room.
Shoot down the stalactite hanging next to some vines so that you can reach them and climb over the gate. Pull the switch above the gate to open it and drop down. Enter the room on the left, defeat the Lizalfos and go out the opposite side. In the room beyond is a Small Key. Go back through the previous room, destroy the boulders with a Bomb and take the next door..
9.3 The Clawshot
Defeat the Chu Worm using Bomb Arrows then unlock the door with the Small Key. Go up to the top of the slope. Climb the ladder and pull the switch to let water flow into the room. Slide back down and swim to the platform in the center. Pull the lever here to let the water flow out.
Return to the room where you fought the last Lizalfos and drop down to the familiar room below. The platforms in here are now moving. Jump onto one and take the first door you reach. Get the Small Key from the Treasure Chest and go back. Jump onto a platform again and take the next door. Use the Small Key to reach a room that is mostly underwater. Destroy the boulder blocking the end of the passage using a Water Bomb and proceed to the next room.
Climb out of the water and look at the ceiling to find the Deku Toad. Kill all the Toados she spawns and watch her shadow when she leaps into the air so that you do not get crushed. When she lands she will be stunned and you can attack her tongue with your sword. You can also throw Bombs or shoot Bomb Arrows into her open mouth with good timing to stun her. Once she is dead collect the Clawshot. Latch onto the switch above the gates with it to open them and leave the room.
9.4 The Second Floodgate
Return to the dungeon’s main room with the Clawshot. Go up the stairs again and run to the opposite side. The switch here looks like the one in the Deku Toad’s room. Use the Clawshot to activate it and water will flow down the stairs to the right hand side of the room. Slide down the stairs, open the door and run beneath the water wheel.
You will enter a room with a large chasm. Jump onto the platform in front of you. From here, latch onto the Clawshot target above the small Treasure Chest and drop down next to it. Cross the gap to the vines on the left using the Clawshot and climb right until you can stand again. Turn around and do the same thing on the vines above. Do this one more time to reach the exit.
Shoot down the stalactite above the geyser and climb on it to jump over the gate. Use the Clawshot to pull the switch, then reach the door on top of the ledge using the Clawshot.
Defeat the Chu Worms and use the Clawshot to reach the vines on the ceiling. Drop into the water and climb out using the vines on the side. Get to the top of the slope, using the Clawshot to cross the gaps. Watch out for the geyser beneath the first gap. Pull the switch at the top to open the floodgates. The Compass is in a Treasure Chest you can reach from here using the Clawshot. Slide down and pull the switch in the middle. Use the vines on the ceiling to get back to the other side. Take the door on the left and head back to the center of the Temple.
9.5 The Big Key
Swim to the other side of the pool of water, run underneath the water wheel and take the door on the right. Go over the top of the gears and take the door on the left. Pull the switch above the gate using the Clawshot and take the door on the other side to return to the center of the Temple.
Go to the opposite side and use move the stairs so that water flows down to the right again. Slide down the stairs and open the door. Go past the water wheel again and enter the chasm area. Jump onto a moving platform hanging from the first gear and aim at a Clawshot target on the second gear. Beware the Keese as they can cause you to fall off. Hang on until you reach the door on the other side. Enter the next room.
Dive down below the surface of the water and swim through the hole in the wall. Swim up and right and destroy the boulder with Water Bombs, or the Bombfish that spawn nearby. Go through the hole behind it and swim down and left to find another boulder. Blow it up and swim to the surface on the other side.
Enter the next room and kill the Chu Worm inside. Use the Clawshot to pull the switch on the ceiling, opening a hatch underneath you. Extend the chain until you are on the floor below, then let go. Open the Treasure Chest to get the Big Key. Open the door below the water to return to the maze-like room you were in a moment ago. Swim to the surface and you will find a shortcut back to the door.
9.6 Twilit Aquatic Morpheel
Use the Clawshot to get back across the chasm and return to the center of the dungeon. Dive into the water and climb out by the Boss Door. Open it and jump into the hole.
There is a Fairy in a pot behind the Boss Door. You cannot use potions underwater but a Fairy In A Bottle will restore your health if you die underwater.
Boss – Morpheel:
Wear the Iron Boots and sink to the bottom of the chamber. Get close enough to lock onto Morpheel’s eye and pull it toward you with the Clawshot. Then attack it with your sword. If the tentacles get too close to you, immediately swing your sword to repel them. After taking one hit it releases Bombfish to try and distract you. Repeat this strategy until Morpheel emerges from the sand.
Morpheel circles the room and will try to swallow you if you swim in front of it. Escape by equipping the Iron Boots. Swim toward it at an angle until the eye behind its head is within range of the Clawshot. Get on its back and attack the eye with your sword until it shakes you off. Do this twice more to defeat Morpheel.