After cleansing the seas of pollutants with the fairy's help, Link can visit Jabu-Jabu's Belly.
Go to Jabu-Jabu
Jabu-Jabu is underwater, to the west of the Zora Village throne room in the present. Swim over to Jabu-Jabu and he will open his mouth, allowing you to swim in. If he doesn't, talk to King Zora in the present to get permission.
Get the Compass
Remember to equip your weapon to the A button to use it underwater. Go north from the entrance and kill all of the monsters in here to reveal a chest that contains the Compass.
Get a Key
Return to the entrance of the dungeon and go west. You can swim over the holes in the floor, so swim over the northeast hole and equip the Switch Hook to A to move the top-left stone diamond to be above the bottom-left statue, then move the bottom-middle stone statue to be below the top-left statue. A key will fall from the ceiling.
Get the Map
Go north one screen and swim onto the yellow tiles. Press B to rise to the upper floor.
Go west and open the chest on the left to find the Dungeon Map.
Lower the Water
Go north, swim north across the water while avoiding the fireballs from the torches, and exit north.
You reach a room with a Like Like and Iron Masks. Go north.
Be careful of Pincers that pop out from the water holes and attack you. Go to the northeast corner of the room and push the lower block right and the upper block up. Exit to the east.
The oddly-shaped objects are spinning blade traps. They will start moving toward you when you walk into their path. Avoid them and go to the right. Use your key on the key block below the stairs. Go up.
Exit to the south. Get past the Iron Masks and Like Like, then go around and use the northwest exit.
Get past the Moldorm and exit to the north.
Step on the button to lower the water level.
Get a Ring
Go back to the stairs and go down. Go south one screen to a screen where a Spark is spinning around the center. Drop down the hole on the right side of the room.
Use the Switch Hook on the pot in the center of the room, then use it on a pot on the left side of the room. Open the chest up above to get a ring.
Get a Second Key
Jump off of the ledge where you got the ring, and exit south. Push the bottommost block to the right and go up and open the chest to get a key.
Raise the Water
Go south from where you just got the key, then east, then north. You will end up in the room two screens north of the dungeon entrance. Use the Cane of Somaria to put a block onto the switch. Go through the door that opens on the right.
Swim around to the short flight of stairs, and go to the left to find stairs to the next floor. Go up.
Go north, then head east through the winding path. Use the northeast exit.
Go up the stairs to the platform on the right, then get rid of the pot, and use the Switch Hook on the pot to the left. Exit to the west.
Use the Switch Hook on the diamond above you, then on the one on the left, then on the one below you, then on the one on the right. Go up the stairs.
Exit north and then go through the locked door on the left.
Step on the switch to raise the water level.
Get a Third Key
Go east, then south, then down the stairs. Use the Switch Hook on the stone diamond on the right, then exit east.
Go up onto the platform and then hop off to the right. Exit to the south.
Go through the winding path and exit to the south. Swim to the east side of the room and go through the east exit. Kill the Moldorms to make a chest appear that contains a key.
Get a Gasha Seed
Exit to the west, then swim to the top-left corner of the room and exit to the north, then exit west. Dive into the deep water. Go around and open the chest to get a Gasha Seed.
Go down the stairs here, then swim around to the room on the right. You will fight Angler Fish. You have to hit the light on its head to hurt it. Hit it with Scent Seeds to deflate it, then go over to the deflated fish and hit the light with your sword.
Get the Long Hook
After Angler Fish dies, go up the ladder that appears on the right.
If you don't have a key for the key block, use the Switch Hook on the stone diamond to the south. Exit south, then west, then north. Hop down to the lower level and go to the yellow tiles on the right. Go to the surface by pressing B. Then go east, then south, then swim to the east exit. Kill the Moldorms to get the key. Then go west, north, west, and dive into the deep water, then swim down the stairs and follow the path east to the ladder that appeared after you killed the Angler Fish. Go up.
Unlock the key block and open the chest to get the Long Hook. This is the same as the Switch Hook but longer. Use it on the diamond to the south. Then go down the stairs to the right, and exit to the west.
Get a Fourth Key
Use the Long Hook to get rid of the stone diamond on the left. Exit west. Then exit north and go down the stairs.
Follow the path until you reach a gap with a pot on the other side. Use the Long Hook on it. Continue along the path until you are back in a dungeon room. Kill the Barinade and Rope in this room. Use the Long Hook on the flower to get rid of it. You will get a small key.
Lower the Water Again
Exit to the south, then go onto the yellow tiles and press B to rise to the surface. Go north twice, then push the lower block to the right and the upper block up, and exit to the east. Avoid the spinning blade traps and go up the stairs.
Follow the path around and step on the switch.
Get a Fifth Key
Go back around the path and go down the stairs. Go south, west, south, then stand on the different-color tile, face south, and use the Long Hook to go to the bottom of the room (if you fall off instead, just exit east, push the block out of the way, then go south) and after you succeed, go east, then jump into the hole.
Use the Long Hook from the left to get the diamond out of the bottom area, then use the Long Hook on the pot up above to get yourself out of the bottom area. Move the diamond onto one of the switches, then use the Cane of Somaria to put a block onto the other switch. Open the chest to get a key.
Raise the Water, part 2
Go east, then north. Use the Cane of Somaria to put a block onto the switch and open the door to the east. Go through.
Swim around to the short flight of stairs, and go to the left to find stairs going up to the next floor. Go up those stairs. Go north, then around the winding path to go north again, then get onto the platform and get rid of the pot, then use the Long Hook on the pot across the gap. Exit west.
Use the Long Hook to reach the stairs in the middle. Go up.
Go north, then use the Long Hook on one of the diamonds across the gap, and go north. Go to the left side of the room, unlock the key block, and go west. Then go south and step on the switch to raise the water.
Get a Sixth Key
Go north, east, and south. Use the Long Hook on the diamond to the south. Go south until you can't go farther south. Climb the stairs and use the Long Hook to go left, then use it to go down, then go east and open the chest to get a key.
Get a Seventh Key
Jump down the ledge and go north twice. Use the Long Hook on one of the stone diamonds to go to the right side. Exit north, then go west, then south. Push the lower left block down but DON'T step on the switch. If you accidentally step on it, just go back through where you pushed the block out of the way, and step on the northernmost switch. Go south.
Go around the path and go down the stairs to the second floor. Go south, west, south, and west again into a room with a chest. Use the Long Hook to reach it. It contains a small key.
Get Another Gasha Seed
Go east, then south, then east. Go onto the platform at the top right and use the Long Hook to go to the bottom platform. Go east twice, then north twice. Go east through the winding path and exit north, then use the Long Hook on the leftmost pot to reach the platform on the left. Exit west. Use the Long Hook to reach the stairs in the middle. Go up.
Go north, use the Long Hook to reach the upper right and exit north, then go west two times. Then go past the Moldorm and Iron Masks to reach the locked door at the upper right. Unlock it and go through.
Open the chest to get a Gasha Seed.
Get the Boss Key
Go east through two locked doors. Get the Boss Key from the chest.
Raise the Water, part 3
Use the Long Hook on the stone diamond and exit west, then south
Reach the Dungeon Boss
From the room with many stone diamonds, make sure there is water in the hole (exit north, then west, then south and step on the switch if not), then use the Long Hook in the diamonds room to get past the short wall and exit south, then go down the stairs. Use the Long Hook to go to the right side of the room and exit east.
Hop down the ledge to the right and exit south. Go around the winding path and exit west.
Press B to go to the floor below you, then swim west onto the different-color tiles and press B to go up a level. Use the Seed Shooter if you want to activate the owl. Go south onto the ledge, then follow it around to the boss door.
Plasmarine swims toward you, so swim away. Sometimes it shoots an energy ball at you. Use the Long Hook on Plasmarine to make it change color. It is vulnerable to energy balls of the opposite color, so if it shoots a red energy ball at you, use the Long Hook on it to turn Plasmarine blue and put it into the path of the red energy ball. It will get hurt. Do the same for the opposite colors. Be careful, because sometimes Plasmarine becomes electrified instead of shooting an energy ball.
Get the Essence
Get the heart container, then go west to get the essence, the Rolling Sea.
Afterward, there will be a cutscene. The Maku Tree is unable to hear the final essence, but she knows that it is in Labrynna.
Go south from Jabu-Jabu. As you go south, a Zora will give you a Zora Scale. You can use the Zora Scale to enter the Sea of Storms.