I've never done a 4 layer board and am not familiar with the process of manufacture for them. Will the external layers isolate inner layers from water if say, I will be putting the board into water for long periods (months) of time?
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No. Ordinary PCB technology does not protect against moisture ingress over the long term - that's actually a very, very difficult problem to solve where joints between different materials exist.

Chris Stratton
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Any references on that? – angelatlarge Mar 14 '13 at 22:43
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Theory and experience. – Chris Stratton Mar 14 '13 at 23:08
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Conformal coating might make the board waterproof. I haven't done this kind of waterproofing. So, this is only a thought. – Nick Alexeev Mar 15 '13 at 02:17
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@Nick -- well you're correct, so it's a good thought ;-) – DrFriedParts Mar 15 '13 at 02:20
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If you coat the entire wetted portion, perhaps. But beware of anything which pierces the coating in that area. – Chris Stratton Mar 15 '13 at 03:43
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Ordinary conformal coating isn't good enough for that. You need to pot the board, (resin, silicon, Polyurethane) or put it in a sealed container. – david Mar 15 '13 at 05:32
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The material most commonly used is FR-4 which is a composite material composed of woven fiberglass cloth with an epoxy resin binder that is flame resistant. Because it's a woven cloth, the water can still go through the edges.

Gustavo Litovsky
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For improved corrosion resistance, don't take the copper all the way to edge of the board, because conformal coating often doesn't cover the board edges. Tent the via's (that will cover one end), and conformal coat. This will reduce (but not eliminate) corrosion on all layers: the top layer will have the worst problems because of exposure through breaks in the conformal coating: problems with the inner layers are rare because the top layer fails first. – david Mar 15 '13 at 05:57