Go into the water section towards Agata and swim until you can see the far wall. Do a Corner Jump the first little corner on the left wall, slow swimming towards the corner and holding forward to get an auto-jump.
Hold up-right or right and do a wall jump AFTER the highest point in your jump. If you do it on the highest point you will hit the ceiling and not make the other side. You can be as low as you want after the apex of your jump, as long as you get the wall jump. Then, finish up by doing an air dash to get on to the ground near the bomb crack. Timing this one takes a bit of practice, but is easy to get down by feel alone.
Because this category skips Cherrybomb getting into Agata early, and thereby skipping lilypad, is done differently. In this method you KT up at the waterway's entrance to land on the platform above. This let's you enter the shortcut from Agata to Shinshu the other way round. Using that entrance it sets you up perfectly for the Agata Bloom Brush Adventure.