Soaked carpet after a rain

First thing I would check is door and window seals. If they are good and window adjusted...
I think mine leaked from almost every possible source. Your description sounds like one of the last ones I dealt with. After doing my window fuzzies, I noticed the same thing was happening-soaked by the sill plates. (I did not have a leak there before I changed the seals:BangHead:)
I removed the inner panel and hosed down the outside. Got in from the other side and investigated. The seal was good against the glass. But, There was water going between the backing metal and the door, down on top of the regulator bracket. From there it ran/splashed against the back of the interior panel and you can figure out where it would go from there. lol
So, I pulled the fuzzies and ran a bead of caulk behind them, which definitely helped
But that's not all... I also added a rubber seal at the back of my glass to fill a big gap.(you may not have this depending on what car you are working on)
Cinnamon 75 Duster \
After all that I still had water getting in so I reworked the seal behind the panel
Cinnamon 75 Duster \