With the door open, run a hose pipe down the out side of the window. The water that gets past the window scraper should run out through the drain holes in the bottom of the door and run over the outer cill. If the inner door panel seal is leaking, or the drain holes are blocked, water will run out from behind the door card, over the inner cill and soak into the carpet.
If this is happening you need to take the door card off and either replace the seal on the inner panel, or squirt a bead of silicone around it, then ensure that the doors drain holes are clear.