I agree with Bruce, the acrylic sheet/thin plexiglass is the method I have seen most use, with success to simulate an above/below surface diorama. As I recall, Shep Paine had a diorama where he used thin plexiglass that he heated (heat gun I suppose) over a formed plaster type base that simulated the oceans surface (waves, etc.). Once the sheet took the shape, he contoured it with either clear silicon caulk or resin type substance and painted it. Nice affect. I don't have the book near me, but when I get a chance I will try and find it.
Also note, Woodland Scenics came out this last year with a product called "Realistic Water, #C1211." It is an acrylic gel and and works great (no nasty resin fumes). So everyone forget about the melting balls. Also, Woodland offers a product called "Water Effects" which has a little more structure to it so you can mold a little more texture into your water (i.e. rapids, etc.). Bought some but have not used it yet.
I hope this helps.
Dmod