There are a few places where the water can enter.
1)Your heater core is leaking and seeping coolant into the passenger footwell, soaking the transmission computer underneath which screws up the shifting and you may need a new TCM(expensive).
2)Your sunroof and battery drains are clogged and are leaking water inthe cabin(easy solutions).
3)Your fresh air filter housing is cracked and needs to be fixed or new gasket needs to be applied.
In my case it was 1) the worst case scenario.. check if you are losing coolant, if not then it's most likely your sunroof/battery drains..do a search on
PassatWorld.com there are plenty of write ups..After you fix the issues pull the carpet and take the TCM out and blow dry it really well, you may get lucky and not need a new one..
Good luck