I have a 95 GTI and when it rains I get water in my front floorboards (passenger side greater than drivers side). I don't have any rust on my car, I can't see water running down from the sunroof, and it is not the heater core.
Check the drain for your A/C if you have A/C. Mine clogged and would do the same thing I could also hear the water flowing when I turned after driving for a while an hour or two. The drain is under the heat shield on the fire wall.
If that didn't work and you're still having problems, check your window seals. The rubber on my window seals dried up and pulled away from the windows, causing water to run into the door, then spill onto the floor of my car.
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