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Would it be more effective to build a nuclear command bunker under a lake to provide protection from a nuclear blast? For example if the U.S decided to build a Cheyenne Mountain equivalent underneath one of the Great Lakes (Avg depth ~100m) or Crater Lake(Avg depth ~350m) with a layer of rock above, how hard would it be to build and would the water provide good protection against nuclear effects?

I would think that the layer of water would provide complete protection from a direct strike since the surface of the water would be vaporized but the shockwave would have little effect on the structures underneath the lake and unlike Cheyenne Mountain the water would just flow back into place afterwards allowing for protection against multiple strikes.
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