Return to the Main Room, top level. From this location you can see a torch down below on the giant wooden flower. Fire an arrow through the flames to light the torch and cleanse the water allowing you to swim in it now.
Stray Fairy Collection
Head to the north side of the Main Room and use the Deku Flower to fly to the northwest corner, step on the switch to spawn a chest at the southern end. Open the chest to find Stray Fairy #10 . Head into the Bridge Room and shoot the bee hive above for Stray Fairy #11 .