After dropping a fish from a bottle in front of Jabu-Jabu, you end up in his belly.
Find Princess Ruto
You can use your Deku Shield in here because there is no risk of catching fire. Walk forward to make two Octoroks attack you. Raise your shield to make their rocks bounce off and hit them. After that, you can toss a Deku Nut to break the bubble-like Shaboms.
Use the slingshot to hit the hanging switch and open the door. Go through.
Stun the Biri (jellyfish) with a Deku Nut and run along the edge and go through the door at the end.
Go forward to find Princess Ruto. She storms off angrily but ends up falling down a hole. Jump down after her and talk to her a couple of times. Pick her up. When going through doors with her, be sure to walk right up against the door. Otherwise, you might end up throwing her accidentally.
Get a Gold Skulltula
In the next room, use a Deku Nut to pop the Shaboms. Set Ruto down near the edge and jump down. Throw a Deku Nut, or walk onto one of the moving things on the floor to make it float up. It's called a Stinger. Use the slingshot to kill it. After killing all of the Stingers (or ignoring them), kill the gold skulltula with the slingshot. Then step on the switch to raise the water. Swim to the vines to climb up and get the token. There is a fairy in a jar on the ledge above that you can catch in an empty bottle if you wish.
Get the Boomerang
Step on the switch to raise the water again, and this time, swim over to Ruto. Pick her up and wait for the water to go back down, then jump down with her and throw her to the other side. Press the switch again and swim across to her. Use a Deku Nut to kill the Shaboms on this side, then shoot the hanging switch with the slingshot, get Ruto and go through the door.
Use your shield to deflect the rock from the octorok. After you kill the octorok, pick up Ruto again. Jump onto the moving platform that eventually floats down. Up above, jump off and go back to the room where you first found Ruto (the door is near the two wooden crates).
Stay close to the right wall to avoid falling down any holes as you go to the far end of the room. Near the passageway to the door at the other end of the room, keep close to the right wall. When the bari falls from the ceiling, just walk past it and go through the door.
When the path splits, go to the right. Avoid the floating tentacles. They are called tailpasarans. They will shock you if they touch you. When you see a switch on the floor, step on it while carrying Ruto to activate it. With Ruto, go through the door that opens.
Drop Ruto and kill all of the Stingers to make a chest appear that contains the Boomerang. You can aim the boomerang by making it so Link's head is in front of the thing that you want to hit. Take Ruto back out of the room.
Get the Map
Go back into the center area with the three tailpasarans and go straight across. Put Ruto onto the blue switch and leave her there, then go through the door that you unlocked (Ruto will still be outside of the door when you come back). Target the thing in the center and start circling around it. Don't go too far from the tentacle or it will rise back up to the ceiling where you can't reach it. Hit it with the boomerang a few times to kill it. Open the chest that appears. You will receive the map. Go back out.
Get the Compass
Talk to Ruto and then pick her up. Take the first left and take Ruto into the room. Drop her, then use Deku Nuts to kill all of the Shaboms. Open the chest to get the compass. Pick up Ruto and leave the room.
Kill the Remaining Tentacles
Go straight through the center area with the three tailpasarans, then before you walk over the yellow switch that you stepped on earlier, turn left and go into the room with Ruto. Kill this tentacle the way you did the other one, then exit with Ruto.
Now go to the center of the area with the three tailpasarans, and this time go right, and carry Ruto through the door that is in the center. Kill the jellyfish with the boomerang, then kill this tentacle. Leave with Ruto.
Get Two Gold Skulltulas
Go back to the big room with holes in the floor. Stay close to the right wall to avoid the falling bari. Drop into the second hole. Set Ruto down and use the boomerang to kill any jellyfish that approach. Use the boomerang to kill the two gold skulltulas and get the tokens.
From the ledge where you and Ruto landed, take Ruto and go through the passageway and go through the door at the end. Throw Ruto onto the platform in the middle. After a cut scene, approach the platform. Bigocto appears.
At the start of the battle, use the boomerang to stun Bigocto and stop it from running into you. When it starts moving again, it will spin around. Stun it while it spins, and if you are lucky, you might stun it when its back is facing you, allowing you to hit the glowing spot on its back. If not, keep stunning Bigocto until it starts running away from you. Stay close to the spikes of the central platform without touching them to get close enough to Bigocto to stun it again, then hit the glowing spot. After you have hit the glowing spot enough times, Bigocto dies.
Get a Fourth Gold Skulltula
Walk onto the platform in the center of the room to be raised up to the second floor. There is a fairy in the pot in the middle. Kill the nearby jellyfish and exit this room.
Go down the slope on the right and kill the Octorok, then go back up to the ledge. Hit the flailing thing with the boomerang. Jump onto it once it's stunned, then hit the next flailing thing with the boomerang and jump across it to the exit.
From the ledge, jump onto the ledge across the way and it will float down to the first floor. Boomerang the jellyfish, then pick up a crate. Put it onto the blue switch in one of the hallways in this room, and go through the door that opened.
Boomerang all of the jellyfish in this room. There is a gold skulltula on the vines in the middle of the room. Hit it and get the token with the boomerang.
Reach the Dungeon Boss
Climb up the vines onto the tall platform in this room. Stand on the far left side of the platform and throw the boomerang so it passes the thin wall and hits the hanging switch. Drop down and go through the door that you opened.
Target Barinade and start circling it. Throw the boomerang to cut one of the tentacles connecting it to the ceiling. Target another tentacle and repeat until you have cut all three.
The floating baris are vulnerable now. Kill as many as you can with the boomerang. Barinade will start circling the room, and if you killed any of the baris, there will be a gap in the barrier around Barinade. Keep trying to hit Barinade with the boomerang to stun it. When it's stunned, kill any remaining baris.
After you kill all of the baris, Barinade will start circling the room again. Sometimes Barinade will stop moving and shoot electricity at you, so keep circling around to avoid it.
Stun Barinade with the boomerang when it starts floating around again, then hit it with the sword repeatedly. Repeat this strategy until Barinade is dead.
Get the Heart Container and step into the light. During the cut scene, you can reply to Ruto however you wish.