Huge Mushroom & Huge Fungus replace both Water and Lava, while tree growth (Azalea, Acacia, Jungle, Oak, Spruce, Dark Oak, 4 x 4 Jungle, 4 x 4 Spruce) replaces only Water.
This does not replace Water Logged Blocks.

Tree Demonstration:

https://www.youtube.com/watch?v=kRk8V2W6rLI
(The Stripped Crimson Stem is to prevent the sapling from being washed away. Command blocks were for testing)

Huge Fungus Demonstration:
https://youtu.be/bG6qka3-mZk?t=89