Question about sea water...

I use a product called "Envirotex" resin (Check the model railroader's sections at the LHS for it) for "see-though" water.  The trick to using it to create those kind of waves is to pour in several layers, building up the depth, then pour the last few layers and tipping the base in the direction of the waves as it starts to set up... It can be tinted various colors with dyes or even food coloring... For the whitecaps, I'd use titanium white oil paint... Once all is in place and set, I then use another coating, "Mod-Podge" high gloss sealer for decoupage projects... It's brushed on and looks like white glue, but dries to a hard, high-gloss finish...

For choppy water, I use crumpled foil over the resin to form the "chop"... After pouring the final layer I press the foil onto the resin, then let it cure.  Be sure to coat the foil with a release agent (I use regular PAM cooking spray) or you'll have a bear of a time removing it.  Also make sure that no foil gets any resin over the top, or you'll have bits of bright, shiny aluminum "floating" in the water forever when you're done.

One caution though... ALWAYS pour Envirotex(or any other clear casting resin) in thin layers, no more than 1/8th-1/4th-inch at a time, allow each layer to cure, and follow the mixing ratios as closely as possible... It generates heat as it cures, and thick layers may not just warp or melt a styrene model, but can actually set it on fire... I lost a Kingfisher that way (and could have lost the house), by pouring a one inch-thick layer and adding a "Little Extra" hardener to speed up the curing process...

For 1/35th "sand", aquarium sand will work nicely, but the best way to use it is to landscape the "beach" in Celluclay or Plaster of Paris, adding tracks and shellholes, footprints, etc., then cover with white glue and sift the sand onto it in a nice, even layer, then pour off the excess.... 

For deep water, I use Plaster of Paris and aluminum foil, with the Mod-Podge poured over the painted plaster.  Here I used plain ol' tempera paint or the colors...

yes envirotex works well.

One additional thing about Envirotex which Hans didn't mention.   Envirotex shrinks as it hardens.   If you run some up against a vertical surface,  like that LCM hull it will cling at the level of the pour then shrink away.  The result is the appearance of water flowing up hill.    Fake it with white frothy waves & wakes dabbed around the edges

Another thing you might want to try is acrylic gloss gel medium - it's what artists use to bulk up acrylic paint. It's water soluable, doesn't really smell, and drys clear. I've used it to make ocean bases for several of my ship models, but never with waves quite that high. You can add it in layers, though, and it doesn't seem to shrink all that much. One nice thing about gel medium, it is easy to "push" it into gaps next to the model and work it into nooks and crannies before it hardens, and to sculpt it into individual wavelets. Below is my take on a stormy North Atlantic in the winter:

As far as the edges go, You would have to use sheet styrene of sufficient thickness so it wouldn't bend to wall off the edges of the base, and coat the inside of it with something that the wave material wouldn't stick to.Since my waves weren't that high (this is 1/700 scale), I just kept nudging each one back to vertical if it tried to slop over the boundary.

For painting, I use a mix of acrylic colors because they dry fast - the ones in this North Atlantic deep water scene are three parts phthalocyanine blue, one part phthalocyanine green and enough drops of dark gray to give it a roiled up, murky color. When coloring water, I always adopt the TLAB approach - That Looks About Right. Mess with it too much and you are guaranteed to mess it up!  

The thing that you need to keep in mind is that it requires a lot of planning. You have to wrk it all out before you do it and anticipate anything that can go wrong...because it will and leave you with a big smelly mess to clean up. Good luck with it.

I have used layers of tinted polyester resin cast on top of Plexiglas sheet using taped carboard walls to stop it running everywhere. Then I cut it to size, polished the edges and glued it onto the base and finally used acrylic gloss medium to fill in any small gaps.