[Sluttypatton]

Water should not be able to enter the intercooler. In order for water to enter the intercooler it would need to go through the air filter, through any piping you have, into the compressor, through more piping, and then into the intercooler. The intercooler is sealed to the atmosphere, if it wasn't your system would leak boost. If by entering the intercooler, you mean passing through the core along with regular cooling air, water wont do any harm.