Isn't the light already polarised when it passes through the water. Double polarising would either have no effect or it would stop any light from reaching the lens. Tell me if I'm wrong.
John, I think he's probably talking about polarization (or polarisation if you are British
) for the top half when doing an over/under shot. That's an interesting dilemma. You are right that polarising the underwater portion would just make it very dark and not provide any benefit at all.
You can of course do some post processing with either Lightroom/Aperture/Photoshop using a gradient filter, but nothing that works exactly like a Polarizing filter. I've often wondered if there would be a market for a Cokin/Singh -type wet filter holder system for U/W photography... Best option for the original poster is to shoot as early or late in the day as possible so the above water light is very nice and won't need any type of filter at all.
But, at any rate, probably the best you can do is use a digital gradient filter with one of the tools I mentioned above.