Before Link brings the water level back to its original height, he must find two more Small Keys to ensure that he doesn't get stuck later in his quest for the Water Medallion.
Briney Brawl
Raising the water level to the halfway point causes a floating platform to rise within the tower. Link can now switch to his Iron Boots and sink into the hole which was previously blocked by the platform.
Bomb the Crack
Link should use the Iron Boots to return to the room where he originally met with Princess Ruto. Replacing the Iron Boots with the Kokiri Boots will allow Link to surface in front of a cracked wall.
Fill the Temple
In the main chamber of the Temple, Link's next move is to unlock the door next to the floating platform. Within this room is a switch which causes another geyser to erupt. The Blue Tektite which falls from the ceiling should be destroyed first, and then Link can ride the geyser to the upper level.