Head to the Sealed Grounds and be ready to fend off The Imprisoned for a third time.
Once you're done, talk to Groose outside and you'll end up in Faron Woods, or what's left of it. Talk to the Kikwi Elder, then swim all the way down to the base of the tree. Enter it, then swim up until you can get out of the water. Talk to Faron, and jump into the water after the cutscene. Charge into the cluster of yellow fish in front of you to get the first eight notes.
Another eight are found on the bottom of the far east section, around a tree. Note that you have to collect them in one circle in order to complete the section, so swim carefuly. Swim west now, past the Parella and air bubbles, you'll see the next one, a big purple fish, inside a tree straight in front of you. It tries to run, but it's not too hard to catch.
Underneath the roots of the same tree you'll find four more (yellow). Start at one end and swim your way through the explosive plants, collecting the notes in one swoop. Four purple ones patrol around the nearby road leading onto the southern cliff.
Continue going west. Past the poisonous bubbles and the parella you'll find another set of purple ones, a grand streak of sixteen notes! Turn right as soon as you finish collecting them and swim a bit, sticking to the ground. You'll see two red ones in a grass patch. North of those two you'll run into a pack of four azure notes. In the area up ahead (With a poisonous and a normal bubble spring on the road) you'll find two purple ones in two nearby grass patches. Swim north, into the north-west region with the circular path and you'll find four red notes patroling around. There's a Blowfish there swimming around a loose wall. Propel the fish into said wall to uncover a big green one.
Continue east now. A bit above the ground you'll see eight azure ones, and around the overlook another four pink ones.
Circle along the big tree and you'll find a big azure one underneath a root, and a big red one patroling the area. When prompted now, head to the Kikwi Elder to get the ability to dowse for the fish. Now, from the elder's lilypad swim west. At the bottom, through a tunel, you'll find eight green ones.
Lastly, go to the surface and swim to the big lilypad east of the Kikwi Elder. Use the hovering plants to get up on the tree, and go up the slope, killing the Bokoblins. Jump down from the edge where the butterflies are, onto the lilypad below. This will flip it and release the big yellow Tadtone, finishing the song. Head into the tree and back to the water dragon, Faron.