Proceed forward and remove your Iron boots to enter the central chamber. Re-equip your Iron boots and proceed to the bottom level of the right wall. Enter the passage here and at the end you will encounter Ruto, who is still harboring an unhealthy infatuation with Link. Remove your boots again and ascend to the surface of the chamber. You will see a triforce emblem mounted on the wall. Play Zelda's Lullaby at the emblem to lower the water level.
Before jumping down, instead use Din's Fire in the middle of the chamber to light the torches in the room. It will unlock the door behind you. Enter the doorway and fight a trio of Stalfos. Defeat them and then use your hookshot on the only panel on the wall in the room. You should do this to every one of those panels you encounter here, so make note of what it looks like. Doing so, you will obtain the Dungeon Map.
Leave the room, jump down to the bottom level and use Din's Fire again to light the torches on the bottom level. Enter the doorway there and fight a trio of Lizalfos, then hookshot the wall panel to obtain the Compass.
Exit and immediately use your hookshot on one of the two pillars to be able to hookshot up to the middle level with the wall already blasted out. Hookshot the panel in the room you find there to get the Longshot.
Return to the central area and enter the middle pillar doorway on it's south side. Inside the pillar, use your Longshot to climb to the upper level. Head to the south-west side of the platform and use your Longshot to pull yourself over to the nearby platform with another Triforce symbol on the wall. Play Zelda's Lullaby to raise the water level to the top.
Head back to the middle pillar in the central room and put on your Iron Boots so you can enter through the middle level doorway. Once inside, remove your Iron Boots and climb onto the floating platform. Play the Song of Time to make a block appear in the center of the chamber, where Navi will glow green. Hop onto the block that appears and use Din's Fire to light the torches in the room. This will unlock the chamber at the bottom of this area. Throw on your Iron Boots and descend to the bottom and through the passage.
At the end of the passage you will come to a chamber with stone walls and boxes. There are two silver switches in this room. You can ignore the obviously visible one, and head over to the two half-high walls tucked in the corner where the second switch is hidden. Hit it, and remove your iron boots to enter the room that was unlocked by the switch. You'll find another paneled wall to Longshot for a Small Key. Return to the central chamber once again.
Use your small key on the only locked door in the room. In this chamber, walk up to the edge of the platform and use your Longshot. Look up to see a silver switch. Strike it, and jump down to the moving platform below. Longshot over to the top-leftmost target. From where you land, use the Longshot again on the left wall panel to raise the topmost target. Longshot over to the raised target and go through the doorway to the next room.
Here, jump down and fight another trio of Stalfos. Defeating them raises the dragon-head statues in the room. Longshot over to the one that was to your right when you entered the room. Navi will go green at the center column. Get to the far platform and play the Sun Song where Navi is green, Catch the first fairy and then Longshot up to the door area, You can then jump diagonally to the ledge on the far side with the three pots. Two more fairies are in the pots. Catch them if you need them. Go back to the high ledge where you must Longshot again over some spikes. Navi will go green in two places here. The Sun Song will call a fourth fairy on the right, The Song of Storms for a fifth on the left. If you miss them or accidently use them up exit through the door you came in and re-enter. They will come back. You will need them. Now enter the next area.
You will find a vast expansive lake with a lone tree and island in the middle. Run to the other side of the area, and then run back to the island to fight... Dark Link! Defeat him with the Megaton Hammer and the room will transform into a plain ordinary room.
Go through the door to the new room and Longshot the wall panel to open the grate beneath it. Hop on down.
Jump in the river here and avoid the whirlpools. Midway through you will have a chance to snag a skulltula, if you're doing that. At the end of the river, Longshot up to the doorway and enter the next chamber.
Toss on your Iron Boots and enter the small underwater room next to the dragon's head statue with your Longshot. Take off your Iron Boots and swim up to the small alcove. You will find another wall panel to Longshot. Use Din's Fire to light the torches to unlock the door. Put on your boots again and go to the next chamber.
Hit the silver switch in the next room to raise the water platform. Jump onto the platform and use Din's Fire one last time to light the torches and raise the gate. Open the chest beyond the gate to get the Boss Key.
Continue down the hallway and put on your Iron Boots to return to the central chamber. Longshot up to get to the exit and step on the switch to unlock the gate. Take off your boots one last time and swim to the surface.
Longshot over to the Dragon Head Statue and enter the door behind it.
In this room, shoot the switch above the boss door to raise a Longshot target. Longshot over and enter to battle Morpha.
Jump onto one of the platforms in this water-filled chamber to activate the boss fight. Return to a corner of the room and wait for Morpha to start conjuring a tentacle. Run to the next corner and use your Longshot to yank Morpha out of his tentacle and give it a slash. Rinse, and repeat a few times to make this boss dry up. Collect your Heart Container and hop into the blue light to get your Water Medallion. Congratulations, you've finished the Water Temple in Master Quest.