Wasn't obvious that was the cause,but as I've experienced the same problem on a MK2 GTI and a MK4(which both had sunroofs and therefore blocked sunroof drains) I figured that there had to be drain channels running from the gutter panel under the windscreen to allow water somewhere to go-else it would just sit in there and cause rust.
I had the problem resolved under warranty as I noticed it about ten days after I bought the car and had to nudge the spannerman in the right direction of where to look,after he just left the car running for two hours with the heaters on full to dry it out....and then proceeded to open the passenger side door and declare all was well,when infact it was the drivers side that was the problem......
So, I think the drains can become blocked with crud buiding up in the holes at the top.I'm not sure where they come out underneath the car but somewhere in the wheelwell/sill area would be my guess.If you find them,just squeeze the end as they can sometimes stick together,if they're anything like the ones on the MK4 that is.