Bees in nature don't have as much problems as some beekeepers add.
I think too much water suggests just the opposit of what you speculate
happened. Bees keep the hive warm in winter. To do this they eat stores and
release water vapor. You do need to arrange for somewhere to let it out. I
would suggest you screen the hole in the inner cover, andd an Imrie shim
above it, with several 1/2 in holes on each side, screened on the inside to
keep other bees and bugs out, and restrict the lower entrance somewhat.
Tilt the hive a few degrees forward. You should have a dry hive in the
future.
 
Cordially,
John F. Mesinger