Use Deku Flowers Offensively
Up until Woodfall Temple, the game only makes you use Deku Flowers to travel along platforms or to get to higher areas. However, there are rooms in Woodfall Temple that require you to use the Deku Flower to hurt your opponents rather than just to travel. The first enemies you are able to do this with are the turtles that you first encounter in the woods looking for Koume. To defeat these creatures, dive into a Deku Flower and pop out just as the turtle crosses over top of it. This will kill the turtle instantly, saving you a lot of time. The Gekko miniboss also rides one of these turtles during your fight with them, so use them to your advantage.
Deku Flowers also offer you the opportunity to drop Deku Nuts on foes while you’re in the air, so long as you have Deku Nuts to spare. While the Deku Nuts usually only stun enemies, they can also be used to kill Deku Shrubs like the ones in the area surrounding the temple.