Take your backseat side panel off on the side that has water on the floor and stick your hand in the gap, If the drain is plugged you'll have water sitting in there every time it rains or you wash your car. Then every time you turn or brake you flood your carpet.
I've had a heck of a time trying to get mine to totally drain right. Someone had posted on here that they drilled a hole at the dog leg area under the car it will fix the problem for them, but I just keep putting that off as a last resort.
Good luck with it.