How can I have ground under water, so that I can see it? The current ways I found so far result in no shadows on the surface so it looks completely flat. Also, under water there should be spots of light that are bright from the waves (displacement), but none are there.
Learning is hard 
PLZ HELP
Is it possible to do it with only one light source?
ok, so your water surface is a mostly transparent plane with the wave modifier set on, right? Then a cup or bowl beneath that is the bottom surface. put an object in between, and the light above should go down through the water plane, shine on the object, and cast a shadow on the bottom. put your camera underwater (no watertight case required) and you should be able to render an initial scene. You can texture the water surface plane with hard clouds to mimic the focusing effect of waves.
Set Transhadow on the ground material and you’ll have light illuminating the ground.
As for spots of light from the waves, what you’re looking for is caustics and you’ll need Yafray, Indigo, ect… for that. You can fake it with textured spotlamps though.
Transhadow made the cube look like a flat plane :(, but its ok I will use YafRay, thanks for the help guys.