Head south and into the closest water source, next to the tree. Dive down and enter the cave. Swim along until you reach a wide open area. Climb up and jump on the hanging platform. Use the bellows to swing the platform in one direction. This way you can reach the second one, and after that, the other ledge.
Once you're outside climb the tree, making sure you get rid of the Walltulas along the way. Once you're on top enter the cave, and get rid (or jump over) the Moblin. Follow the path up the tree, it's straightforward. Once you reach the top a cutscene will trigger. Hit the sleeping Kikwi with the Beetle or slingshot to awaken it. After the conversation, jump down and go to the Overlook, where the hermit marked the X on your map. Stand on top of Farore's symbol on the ground, and Fi will prompt you to call her.
Now head to the far south, as far as you can, to the cliff overlooking the small lake. There you'll find a tablet with the incomplete version of the symbol you just saw. Stand in front of it and charge up your sword. Now draw a circle on the left side, where it's normally placed on the complete symbol. Head forward and jump down into Lake Floria.
Dive down and follow the only path available. Follow the Parella as it flees, and talk to it in front of the wooden gate. Shake your nunchuck to break said gate and move on. After a short conversation and a trip down a linear tunnel you'll be in a small underwater chamber. Charge into the Blowfish to ram them against the loose wall on the north side and open up the path ahead. Dash to leap over the gate when you reach it. In the next chamber, you'll have to leap up on the ledge and dive into the next region. Continue following your escort. Up ahead you'll face Scarfish!
Enter the door once the Parella opens it and head to the center of the chamber to meet the Water Dragon, Faron. Once you finish the conversation, head out of the door and take a right to get back to Faron Woods. You now have to go all the way to Skyview Temple. Once inside, go through the dungeon as you would normally until you reach the hub with the four doors. Go through the top right one. Jump inside the water, dive down and swim through the small opening. Dive out and dig a few times into the mound to find the small key. Go back to the central hub chamber and through the door. Nothing much to do in this room, so just head right, as you'd normally go if you were going to the boss room. The path is pretty straightforward. Once there, you'll have to fight three Stalfos at the same time, the most challenging fight in the game up to this point.
Once they're dispatched off, enter the spring area and dowse to pinpoint which spring is the Holy Water one. Scoop some water with an empty bottle, you'll be teleported outside afterwards. Head back to Faron via the log you pushed down in the south-west part of the woods. Talk to Faron and she'll open the way to the Ancient Cistern. You'll have to leap out the water to get up to it.