2 other possibilities:

1-rust hole at the bottom of the A pilar;
2-you'd be surprised how much water gets carried in by getting in and out the car in rainy weather. It goes through the carpet and soaks the sound deadening underneath, this will not dry automatically! Take the sound deadening out an leave it to dry, this will take some time. At the same time you will have the opportunity to check out the floor situation.

Cheers.