Glen,
I did some digging and found a black&white photograph of my former N scale layout where my glass lake is (more or less) clearly visible.
First I modeled the bottom of the lake like the surrounding terrain, and the color went from the reddish tan of the surrounding rocks to a murky brown at the deepest part of the lake. Then I 'planted' underwater weeds and algae patches (visble as darker splotches on the photograph) plus a few details like battered oil drums and other junk.
Then I covered the lake with a glass plate which I had sprayed with transparent blue paint from below. This is better than paint on the upper surface: From time to time you have to clean away the dust which gathered on the glass, and this way the paint won't be scratched at all.
Finally you have to work down the surrounding terrain to the glass plate so that it exactly matches the underwater scenery. This is a bit tedious, but it can be done quite well.
Of course Alan is right - you have no waves at all. In my case this didn't disturb me, since a little pond in a hollow like this might be dead calm. A harbor might be different, I don't now. (The nearest sea harbor is about 250-300 miles away!

) Perhaps waves could be added by applying wavy lines of acrylic gloss medium on the surface. This is just an idea, I didn't try it!
Val, I think in this case glass is the better choice. Compared to glass, Plexiglass tends to be electrically charged and therefore attracts much more dust. On the same layout I had another small pond (only about 3"x4") and covered it with a painted clear plastic sheet. Every week is was covered with dust

, so I tore it out after about three months.
Ron