One of the most important items in almost any Legend of Zelda game are Empty Bottles and Skyward Sword is no different. There are 5 Empty Bottles in Skyward Sword and the great thing in this game, is that two of these empty bottle can be obtained before even entering the first temple, and the third bottle soon after.
As soon as you have your Sword and Shield in hand, head on over to the Bazaar in the middle of Skyloft and speak with Luv, the owner of the Potion Shop, and she will inform you about her potions. After noticing that you don’t have one, she will provide you with an Empty Bottle that she was storing.
When you enter the temple at the Sealed Grounds for the first time, before speaking with the old woman at the top of the stairs, look over to the right of the stairs. Here you will find a small brown chest, and inside will be your second Empty Bottle.
Bottle #3 can be obtained by completing the Missing Sister Side Quest, which becomes available after completing the Lost Child Side Quest. NOTE: Lost Child should be completed ASAP as it unlocks the ability to perform additional Side Quests that yield great rewards that will be extremely helpful throughout the rest of the game.
Once you obtain the Mogma Mitts in the Fire Sanctuary, in the same room is a hole that Link must travel through in order to get through the gate blocking his path. Once Link emerges there will be a hot dirt mound in front of him. Use the Gust Bellows to clear this mound and reveal another hole. Burrow through this hole and activate the switch to open a gate; once emerged, travel through the gate and make an immediate left. Travel up the stairs and turn left to cross the bridge and enter the door.
To the left is another hole in front of a closed gate. Take Link underground and hit the switch to open the gate above you; this will open a new path filled with water plants. Use the switch nearby in order to open another gate and poke one of the water plants to skewer it with your sword. Head through the gate and make a right. Slash at the Lava Hands to toss the water plant at them to kill them; this will lower the lava level giving you access to a new path which ends with a chest containing your fourth Empty Bottle.
This bottle is located inside a Goddess Cube Chest that becomes available after striking a Goddess Cube in the Eldin Volcano. The tricky thing is, this cube cannot be reached/seen until the second trip to this location. NOTE:More details will be added about this bottle location shortly.