For some reason, it made sense to me.
If i'm reading this right, he basically wants to create a big block of water. On top of that is all glass so that people walk above the water but can look down into it. In the center is a hole in the glass so that people can jump down into the water.
The problem is that people standing on the glass and looking down into the water don't see into the water (which is what he wants) but just see the surface texture of the water. The issue is that in order for Hammer to see that block as water, it needs to have a water texture applied to it, which automatically makes the top (i.e. the part people are looking down through the glass at) have the water texture. Thus, no-body can see through it into the water below.
I believe the best way to solve this would be the way CapellanCitizen said, by creating a material that is water but has no top water texture.
EDIT: Basically, like this, except he wants the water that is under glass (around the blue hole in the center) to be see-through-able for someone standing on top of the glass: