Hey Alex
The one time I did water, I used a clearcoat called 'Polycrylic' by Minwax. It is a really easy product to use. I added Tamiya blue to it (since it is an acrylic, I had no trouble mixing Tamiya paints with is) and then poured it onto my base in thin layers (no deeper than 1/8" at a time). The nice thing is that, since it is a clear coat, you can really vary the sense of depth and the color of the water easily. It also dries pretty fast so you can build up your layers rapidly. Since it is clear, you can also paint your base a sandy color if you are simulating shallow water - even with the blue paint added, it is still semi-tranparent if you use it thin enough.
I got a can of the stuff at Home Depot for about $5 - $10. It is in with the other stains and comes in a can with a blue label.
I'll tell you, if I could do it, then this stuff MUST be pretty easy to use!!