Simply continue forward. Eventually, you’ll get to that ledge from before. If you remember, after you went across it, you found a unarmed Bokoblin. Well, he isn’t there anymore - he was replaced by a Wingless Mothula.
I expect that you know how to defeat it. Defeat it and proceed towards the massive cracked rock. Grab your Bombs and place one beside it. Wait for the Bomb to explode, taking the rock with it. It seems that the rock was covering a hole. Go into the hole.
Inside, you’ll find that you are in a small crystalline cavern. In front of you is a pool of water. Approach it and you’ll see a fairy, which will turn into a larger fairy. This fairy will bless the ability to hold more Rupees upon you, a maximum total of 1,000!
It also allows you to use the fairies here to heal yourself when you become fatigued. This is the general order of events that occur when you enter a fairy shrine on an island. I want you to note this: the fairy allows to use the fairies in the shrine. Therefore, you are allowed to put one in a bottle.
From here, you can go either way to exit the forest. The path to the right will make you fight two Moblins; the other will make you fight the Wingless Mothula again. I assume you can find the exit.