Empty Lake Hylia
There are a few things that you can do before you head to Lake Hylia to complete the Water Temple and one thing that you need to do beforehand as well (obtain a Zora Tunic).
Stock up on Blue Fire in the Ice Cavern and then head back to Zora’s Domain. Use some of the Blue Fire on the frozen Zora King and he will give you a Zora Tunic as a reward.
You can use the Iron Boots and the Zora Tunic to obtain another Heart Piece:
Heart Piece (Zora's Fountain)
Using the Iron Boots and the Zora Tunic to find a Heart Piece at the bottom of Zora's Fountain.
Go back into the Zora’s Domain at night (use the Sun’s Song if required) and travel down the tunnel that leads to the top of the pool where you met the Zora that initiated the Diving Game when Link was young. Around the left corner is a Gold Skulltula that you can reach with the Hookshot (number 76 of 100).
It is at this point in the game that you can complete all of the requirements for the Biggoron’s Sword Side Quest. Check out the link below for more information:
A quest to obtain the strongest sword in the game - similar to the Giant's Knife but unbreakable.
If you have been following the guide all the way through up until this point you should currently have the Prescription in your possession (which you received from the Biggoron at the top of Death Mountain). Approach King Zora and provide him with the Prescription. King Zora will read the Prescription and will provide Link with the ingredients to make the Eye Drops that Biggoron requires. The King will give Link the Eyeball Frog.
The Eyeball Frog needs to be transported to the Lakeside Laboratory at Lake Hylia as quickly as possible (3:00 minutes). Unfortunately you cannot use the Serenade of Water that Sheik just taught you to warp to Lake Hylia as a shortcut – you have to run there on foot.
Run down the stairway leading out of King Zora’s Chamber and follow the river bed down the Zora’s River. Hop on Epona and ride to Lake Hylia. Use the video below to help guide you:
The next step is to take the World’s Finest Eye Drops back to Biggoron at the top of Death Mountain. This run also involves a a time limit (4:00 minutes) and it pretty much requires you to have planted a Magic Bean Plant in the mound of soft soil in front of the Dodongo’s Cavern in order to make it up in time.
Ride Epona out of Lake Hylia and back to Kakariko Village. Run through to the Death Mountain Trail and then ride the Magic Bean Plant up to the top of Death Mountain. Run towards the climbable wall and use either your Hookshot or your Fairy Bow to kill all of the Skulltulas on the wall and then climb up to Biggoron. Use the video below to assist you:
Biggoron will provide you with a Claim Check to come back and claim the sword at a later date. You have to wait three days in total but you can use the Sun’s Song to speed the passage of time. Play the Sun’s Song 6 times to make 3 days go past and then present the Claim Check to Biggoron again to receive the Biggoron's Sword as your reward. The Biggoron's Sword is much more powerful than the Master Sword but it requires two hands two wield. This means that Link will not be able to use his Hylian Shied while he has the Biggoron’s Sword equipped. The trade of is well worth it though and, other than in a few specific cases which will be pointed out in this strategy guide, I highly recommend that you use the Biggoron's Sword for the remainder of the game.
There is another Heart Piece that you can obtain with the Iron Boots:
Heart Piece (Hyrule Field)
Use the Iron Boots to sink to the bottom of a pool to obtain another Heart Piece.
Warp to Lake Hylia using the Serenade of Water and return to the Lakeside Laboratory. Jump into the pool of water and equip the Iron Boots. Roll into the nearby crate to reveal a Gold Skulltula. You can’t use your Master Sword or Biggoron’s Sword while under water, so equip your Hookshot and use it to defeat the Gold Skulltula and then grab the token (number 77 of 100).
Walk down into the middle of the empty Lake Hylia and look for an entranceway. Equip your Iron Boots, sink to the bottom of the water and then use your Hookshot to aim up at the crystal switch above the doorway to open the passageway through into the Water Temple.