First of all, notably I have several stacked beveled shapes above and beneath the water's surface. Of those layers 'below' the water surface, I place blue rectangles between each layers with 50 - 90% transparency applied, so you can see the layer below. With additional shapes of blue transparency above it, the transparent and ground layers beneath get darker blue. Finally at the water surface, I place a repeating bitmap image of water refraction - its basically a painted white lines on blue to emulate water.

Here's the next map for this adventure. This one is a wider perspective with a different scale applied.

Click image for larger version. 

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