I use stacks of transparent layers to create the effects of depth in water, in my maps. I create several stacked layers of terrain: beach above water, beach below the surf, sea bottom in the lagoon, lower sea bottom past the coral reef, muddy sea floor at deeper levels. Then I place rectangles of varying shades of blue with varying levels of transparency anywhere between 20% to 80% transparency. These rectangles are placed below each subsequent sea floor level. Thus the deeper areas are getting progressively darker blue, less transparent, and colors fade to nearly non-existent. Very much as vision and color is lessened the deeper you go.

Here, check out my Ryukyo, Sea Dragon City map. Although the final map is in the Finished Map Forum, you can see some of the steps of development in the WIP forum.