I have a '98 Grand Prix that started leaking water to the passenger floorboard during severe rainstorms. This happened about a year ago. I took it to the dealer and they checked the A/C and found nothing plugged up. At the time the molding around the windshield on the passenger was loose. However, that didn't seem to be the cause either. They thought it might be a cowl leak and told me to take it an auto body/glass place. The auto body/glass place looked at it and said it wasn't a cowl leak but that it appeared a was missing near the vents for defrosting (underneath the wipers). When a hose was run over this portion of the car water would run in on the passenger side footrest. The body shop even demonstrated this for me with the carpet pulled up. They said I should go back to the dealer and ask about this apparent missing piece. Went back to the dealer and they said nothing was supposed to be there. They even showed me a new Grand Prix to compare to.
I ended up going back to the body shop and paying $300 for them to make something to run the water another way by the vents and I haven't had a problem since. Wasn't happy, but it was raining a couple of times a week and I was tired of bailing out my car.