Deku Palace
This next part of the game will take you through the Southern Swamp and into the Deku Palace and Woodfall for the first major dungeon of the game.
On your way to the Swamp, be sure to stop and climb up the large tree to get the Heart Piece at the top.
As soon as you enter the swamp, head left through the water until you come to a large pot and a sign with more pots on it. Go through that canyon to come to the witches' store. Here you are able to buy healing potions and such, but there is a way to get a free bottle here as well as safe passage to the Deku Palace.
Go into the cave behind the building to encounter a little monkey who will ask you to follow him. The following sequence is just like the Lost Woods in Ocarina of Time, but the directions that the monkey moves are always the same. However, if you return here on the second or third day, the directions will be different.
At the end of the trip, you will encounter an injured witch. After speaking to her, return to the building and climb up to the entrance. Speak to the witch inside, and she will give you a potion in a bottle to take to her injured friend. If you have played Ocarina of Time, you will notice these are the same duo that formed Twinrova. Re-enter the cave and follow the above directions back to the witch, give her the potion when prompted and she will be healed. You will also get to keep the bottle, which will be useful later on.
Exit from that area and back into the main swamp. Run back the way you came in and climb up to the large building. There is a Deku up there who will sell Deku Link some Magic Beans (once Link learns how to use them, which will be soon), but your main goal here is inside.
Enter the building and go to the small shack in the corner and speak to the witch inside. She will give you the Pictograph Box, as well as allow you to ride her boat, which will take you to the Deku Palace. Along the way you might see some giant Octorocks but if you don't want to get hurt we suggest that you don't go near them due to the poison in the water around them. You'll be able to get rid of them later.
Since this Palace is for Deku only, you'll need to be Deku Link to get in. Go straight ahead and enter the throne room. Speak with both the King and the Monkey, and snap a picture of the Deku King while you're at it, then exit.
The doorway to the right of where you came in leads to a maze where you have to avoid guards (like in the castle in Ocarina of Time), that ends in a hole that will lead you to the Magic Bean seller. If you head through the other side of the garden, you can find a Heart Piece at the end of the maze. After buying the beans, you need to plant them in a soft patch of land, and then water them with a bottle of spring water (one of the many uses for the bottle). Fill up your bottle with some water in the pond, plant the bean in the tan square and then water it. A large plant will appear that you can use to reach a chest high on the wall, which contains some rupees. Fill up the bottle with more water to use later and buy more beans, then exit out of that area.
Leave the gates, and hop across the lilypads to the right of the boards to come to a small area with another patch of land where you can plant another bean. Do that and water it to form another lift. Ride it up to find a flower shooter. What you need to do, is launch yourself from flower to flower until you reach the cave opening that will lead you to the monkey's cell. The only opposition you will find will be Deku Shrubs on about every other platform, which will fire off Deku Nuts at you. You can either bomb them from above with a nut of your own, or fire a bubble at them before gliding to their platform.
The second strategy is a lot safer, thus is the recommended one. When you reach the Monkey's Cell, show him the Ocarina and he will teach you the Sonata of Awakening, which will open up the entrance to the Woodfall Temple. After Link is tossed out of the throne room, once again leap on the lilypads to the right, but this time head to the small ledge. From there, you need to glide from giant flower to giant flower while avoiding or killing the giant bugs flying around. Before you continue on, consider showing the photo of the Deku King to the man at the tourist shop. He'll give you a Heart Piece, but only if the temple hasn't already been cleared.
Halfway through the area, Link will meet up with the familiar owl that is standing on a tablet. After he flies away, examine the tablet to learn the Song of Soaring, which will allow you to travel to any owl statue that you have hit with your sword - a very handy song.
After you reach the Woodfall area, hop to the area to your right, and follow the walkways (while defeating the enemies on the way) to the platform in the center. Switch to link and hit the Owl with your sword and then use it to save your game. Then stand on the center marker, put on the Deku Mask if you're not already wearing it, and play the Sonata of Awakening to reveal the entrance to the Woodfall Temple. Finally, switch to Deku Link to glide over and enter the dungeon.