Hi--
Could be your windshield. If it were recently replaced they might have done a poor job of sealing it. Just take it to a glass shop and have them look at/test it. I bought my car with this problem--passenger side only--and ended up replacing the windshield (~$200). It's kind of weird how you don't see any trace of the water coming in--just soaked carpeting. Also, check your glove box--I would have water standing in mine. :)
Regards,
ron h