Easy! Just go all the way to the bottom, follow RUTO and she'll disappear. Then, from the second floor in the RUTO room, play Zelda's Lullaby to lower down the water level. From the same floor, side-jump in an angle to the lower chamber, you should land in a room with cracked wall. Drop a bomb and get the key.
Then, open the door in the center column in the central room. Use hookshot to reach a platform with Triforce emblem, play Zelda's Lullaby to raise water. Drop to discover a secret bottom chamber, grab the key, save and quit to respawn at top floor. Use roll-jump to reach a platform with Triforce emblem, play Zelda's lullaby to raise water all the way up, then, with two keys you'll be able to reach the room with the Longshot. Defeat Dark link, get Longshoot, go to the next bottom room to retrieve Boss Key, save and quit. Then reach the Boss room with Longshot, and defeat Morpha.