Speak to the King of Red Lions, play the Wind's Requiem and sail north-west to reach the Greatfish Isle.
The King of Red Lions will tell you about Jabun, the Water Spirit, then Quill will arrive and give you more information. Since there's nothing else to do on this island at the moment, get back on your boat and head back to Windfall Island while doing your best to avoid the whirlpools.
Take a look at the mailbox to read the message. If you want to, you can get in the city to talk to the bar's customers located north of the island, trade 15 green jellies for a potion at the chemist's, and/or go see Lenzo who will offer you to be his assistant. In any case, go to the Bomb Shop south-west on the map, get past the ledge behind, climb the vines and crawl into the passage. The Bomb seller is being confined and robbed by some pirates. Listen well to their conversation and don't forget their password. This password changes from one game to another so we can't help you! Upon their departure, leave the shop and go north-west of the island. Jump on the pirate ship and open the door. Give the password (beware as it is case and accent sensitive), and get in. Take the stairs and Niko will give you a new test. The goal is the same as before, but the run is harder this time, especially the last jump. Pick up 30 Bombs from the chest, then Tetra will advise you to sail back to Outset Island. Leave the boat, go back to yours, but pick up your mail from the mailbox. You will get Beedle's Chart.
Make the wind blow south-west and sail to your beloved Outset Island.
Pay a visit to your grandma, then to the wise Sturgeon and to the boy who lives in the eastern part of the island. Then climb the eastern hill to see that the bridge got destroyed. Climb on one of the two fences that kept the bridge hanging, adjust the direction of the wind if needed, and use your Deku Leaf to fly to the other side and get into the Fairy Forest. Go towards the rock next to the panel, drop a Bomb next to it, then jump into the hole. Walk to the middle of the fountain, the Great Fairy will appear and give you a bigger wallet, allowing you to have up to 1000 rupees. Grab a small fairy in your bottle, get out and leave the forest. Go back to the village and take a look at the mailbox to read an ad about the Rock Spire Island. Go back to see your grandma, and show her the small fairy. She'll give you some Elixir Soup! (This can be done later)
Go back on your ship. Sail west around the island and you will suddenly see a huge whirlpool. Throw some bombs at the huge bright rock. This rock is made of four blocks, blow them up from top to bottom and do your best to get one of them off for each whirlpool run. When the rock (and the whirlpool) disappears, get into the mountain.
After talking with the King of Red Lions, Jabun will entrust you Nayru's Pearl, the last of the three pearls. Your boat will then tell you that those pearls must be placed at precise locations so a new place can be revealed.
Take a look at your map and you will see three points indicating your next directions. Have the wind blow north-east and you will see the first point (D5). Beware of the enemies, land on the island and get close to the statue. After placing Nayru's Pearl, get back on your boat and sail towards the next two points to place Farore's Pearl and Din's Pearl. Once it's done, the three fairies will emerge from their clay armour and will draw the famous Triforce triangle that will reveal a giant building.