I've never heard of anyone doing this, so I don't know if it's possible.
If you're just using it to make a map you can open your world space in the http://cs.elderscrolls.com/constwiki/index.php/Heightmap_Editing and change the mask colors to make your land and water whatever colors you want. Just play around with the elevations and colors until you get something that looks good, take a screenshot and edit it in your image editor. You could get a map with elevation or just change the elevation on the masks to make your water one color and your land another.
You could also try using the http://cs.elderscrolls.com/constwiki/index.php/Create_Local_Maps if you have a small world space, but I don't know if it renders water; in any case, it would only render the editor water so you'd have to change it in an image editor. You might also want to turn off your borders and markers before doing this.
Only way I can think of to make a map with water that looks like the water in-game is to take a screen shot of the water and cut/paste it in an image editor in the appropriate places.
Good luck.