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.