1) just create a brush with the nodraw texture and apply any tf2 water texture to the top face (scale it to 1). For reference have a look at the
official maps
2) such ground is created using displacements and the blending with the Paint Alpha feature of those. You can find the tutorials subforum
here
3) I wouldn't suggest to just copy it but rather understand the entities that are needed and place them yourself. Again for reference have a look at the official maps.