First, I'd direct you to the wiki article for making colormaps so you can give the underwater areas their tint (
https://wiki.srb2.org/wiki/Linedef_type_606). Remember to tag it to the water's control sector instead of the sector the water is in.
Second though, and this is more important for improving these levels, I'm going to talk about texture use.
See, the most important thing about textures is that they're how you make platforms and other important geometry stand out from the background, and special walls from normal ones like in bouncy level. It's a pretty common issue in this pack where there are platforms which are very hard to see, because they use the same textures as the surrounding walls. Wherever possible, you want to use a different texture for your platforms from the background they are next to so they are easily visible.
Similarly, when some walls have special properties, like the bouncy walls in bouncy level, you want them to use a texture that's unique, which the player can recognize as having that special effect. Bouncy level just uses GFZRock and GFZWall for the bouncy areas, but it also uses them for the non-bouncy walls too, so you should consider picking something different so that it's clear what is bouncy and what isn't.