I wish I had seen this sooner! I had the same problem with water running all the way back to the rear seat and it destroyed the carpet padding.
Turned out it was a slightly split seam where two body panels came together. The water coming out of the drain holes below the windshield would run down the seam and in through the hole in the seam. You have to thank the wonderful freeze/thaw Wisconsin weather for pushing it open.
I found this out by pulling the passenger splash guard off and shining a light on the inside of the wheel well and looked from the inside of the car to see where it was coming through. I also made a couple of trips to the car wash with the carpet up and seat out to see where the main source was flowing from.
I used a body panel seam sealer and pasted it all over the inside of the seam. The problem was getting it high enough on the seam because it went right behind the blower motor. Since then (about a year ago) I have had no water problems at all. Hope that helps, good luck!