The shader uses a procedural Voronoi Noise and SDFs for the object intersections.
VFX Artist Harry Alisavakis demonstrated a gorgeous water shader made in Unity that looks like it was taken straight from a Studio Ghibli movie. According to the artist, the scene runs at 120 FPS, but everything was made intentionally choppy to fake the hand-drawn effect.
The desired effect was achieved by using a procedural Voronoi Noise, adjusted from this tutorial, along with some displacement. For the intersections of the objects with the surface, the artist used SDF textures. For the border effect, the author uses a custom post-processing edge detection comparing depth and color values; jiggling comes from displacing the outlines buffer before compositing it.