Paint the base the area you want
watered with a deep blue.
Using a deep green, "blotch" the blue
area while the blue paint is still wet. This simulates deep water.
Using lighter blues and greens (mix each with some
white paint), follow the same pattern towards the edges of the area,
simulating shallower water. Use a bit more green, as water tends to
be more greenish towards the edges. You can even use a little bit of
brown at this time, it will look like a sandbank.
When satisfied, apply a layer of clear varnish.
Repeat the above steps, alternating layers of
paint and varnish. Never completely cover the previous layer of
paint with a new layer of paint. This offset in the layers of paint
is what creates the illusion of depth.