Use your slingshot to shoot the uvula hanging down from the ceiling and unblock the door. Go through the door. In this room you'll first meet Bari. Don't hit them with you're sword, you will get electrocuted if you do. Now follow the path around and just ignore the elevator platform and the ledge in the wall. Instead go through the next door and in this room, fall down the farthest right hole, you'll meet Ruto. Talk to her twice and she'll demand you to carry her. Now go through the door behind you and follow this passageway. At the end is a room with a switch in the middle. Throw Ruto to the other side and then step on the switch to raise the water. Then join Ruto on the other side and follow the next passageway to a blocked door. Shoot the thing hanging from the ceiling to unblock it and go through. In this room wait for an elevator platform to lower and ride it up. Go through the door and you'll be back in the pit room. Avoid the holes and go through the door on the opposite side of the room. 

Now head straight right and hug the right wall until you find a switch and a blocked door. Make sure you're holding Ruto and step on the switch to unblock the door. Put Ruto down in the entryway of this room and go and kill all the stingers in the room. Use a Deku nut on them then hit them with your sword. When they are all defeated you'll get the boomerang. Now you can kill the Bari easier. Pick up Ruto and leave this room then go straight. When you come to a switch. Place Ruto on the switch so she'll hold it down and go inside. Kill the tentacle by Z-targeting and throw your boomerang at it. You will get the map. Now leave and pick up Ruto, and take the first left and go through the door. Kill all the bubbles using Z targeting and your boomerang before the time runs out and you will get the compass. Now leave the room and head back to the room where you got the boomerang. 

Take the side path right before the door to the boomerang room and kill the tentacle here. Leave the room, take a right, then take another right and you'll be going down the center path. Go through the door to find a third tentacle you have to kill. Go back out the door and go straight and back through the next door to return once again to the room with the holes. Now you have to fall down the pit to the farthest right (the one that had the green tentacle through it). You will find yourself in a room with a bunch of jellyfish and two gold skulltula's. Now go through the passage and door behind you to get to Bigocto's room. Throw Ruto up onto the platform and then you'll have to fight Bigocto. Hit him with your boomerang to stun him. While he is stunned hit him in the green spot to hurt him. When he gets unstunned he'll start spinning around. Repeat this routine until he's dead. Jump up onto the platform once Bigocto's dead and you'll be lifted up to a new room. 

Go down the only passageway and door and you'll end up in a room with weird red blocks that resemble Jell-O. Hit it with your boomerang and they'll turn hard for a bit. Make your way to the door on the west side of the room by jumping on the blocks. In the next room jump across the gap to the platform and it will lower you to the ledge with the switch you saw at the beginning. Go pick up one of the crates and place it on the switch. Go through the door that opens. Kill all the jellyfish there and climb up the vines to the high platform.