polyurethane doesn't waterproof wood?

I have aluminum frame windows that frost up in the winter, thaw and discolor the wood window sill.
Thinking that polyurethane would waterproof the sill, I sanded out the water stain, restained the sill, then coated it with polyurethane.
But the next winter, the thawed water still discolored the wood stain in the sill.
Is there something other than polyurethane that could create a thicker waterproof coating on the window sill and seal the joint between the window frame and the sill?
I know turning up the heat or using a dehumidifier could solve the problem, but I'm looking for a cheaper (long term) solution. Replacing the windows with vinyl frame is too expensive, however.
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It would work if you could coat the wood on all 6 sides.
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On 11/25/2010 7:35 PM james spake thus:

You could try epoxy. Specifically the marine stuff people use for boats. I used it recently to coat an exterior door surface. Works well, though there are some gotchas. Not cheap, but it should make the wood pretty water resistant.
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Was the polyurethane oil-based or water-based? If it was water-based, I would try some oil-based polyurethane on a piece of wood, let it dry thoroughly, and then put water on it to see if the oil-based polyurethane works better than the water-based version.
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There's a reason they don't recommend polyurethane for outdoor use. (I don't know what that reason is, but there is one)
Spar urethane, however, comes in outdoor versions. I've used that on windowsills in wet locations (over the kitchen sink, for example). Alternatively, use something that's recommended for decks, although you might have to recoat it occasionally (at least, the deck stuff doesn't last too many years on a deck).
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james wrote:

Polyester resin, AKA fiberglass resin. This would also allow you to reinforce it structurally (with fiberglas cloth/matting) should you see fit.
Before you mix up the batch to use, mix up a test batch first, so you can see how much hardener/catalyst to add (the instructions are just a guide, each application has it's own requirements).
Jon
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I dont think you can since the window covers the woods edge, the edge you cant poly, thats where water is getting in. Wood frames are best.
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james wrote:

More coats = thicker coating. Three minimum, be sure it has a UV inhibitor; even with one the finish will deteriorate especially so of the sill gets sun.
But your real problem is where the sill touches the frame and urethane isn't going to do much there unless you take up the sill and finish it well. About the best you can do otherwise is to run a bead of clear silicone caulk along it after you finish the sill surface. Be sure to mask both sill and frame, silicone is messy and hard to get off.
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You don't want 'thicker'. You want an impervious bond. An oil finish will soak into the wood better.
Someone mentioned polyester resin. I think I'd go with a marine epoxy if this is a troublesome window.
I like these guys-- http://www.rotdoctor.com/ Their product is far from cheap-- but you'll only have to do it once. Their resin will soak into the wood a long ways and outlast the house.
I replaced a piece and treated the bottom of my garage door 8 years ago & I still can't tell where the joint is- and the door is solid.
Jim
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james wrote: ...

Storm windows or if really cheap, the stretchy film route.
Condensate is undoubtedly penetrating under the poly on the side more than actually penetrating thru as ransley points out.
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On 11/26/2010 10:03 AM, dpb wrote:

A single coat of clear finish is generally not enough to seal up the grain. More coats (2 or 3)would likely be the answer, and thinning it slightly may help it penetrate. With clear coat, the wood may still darken from the sun.
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On 11/25/2010 9:35 PM, james wrote:

Spar varnish.
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