You probably already know how to change the water colors but just in case you don't, from the upper left menu go Settings > Terrain Type Settings and click the Change Ocean Color button. I don't remember the default numbers but the ones I used are:
Ocean Color: Red 10, Green 48, and Blue 36.
River Color: Red 46, Green 51, and Blue 10.
With 0 Deep Ocean selected in the Terrain Type, clicking the Change Selected Color gives:
Color of Deep Ocean: Red 46, Green 59, and Blue 84.
Again, I remember playing with the Ocean Color but don't remember what the default values where or if I changed the colors for River and Deep Ocean.
As you guessed, I did create water textures (wntt00xx) for 01 and 03 thru 11. Some of the textures where for the rivers and others for the ocean. The textures where kept small, 256x256, to try and keep the terrain size small and it reduces the details to what you might be able to see if looking through real water.
The beach water texture, wntt0010, is light in color and turns darker in deeper water. By varying the water depth, I attempted to create "surf" but did not use the coral texture.
