A common problem with older VAG cars is the seal of the inner metal door panel. The one that the window regulator is fixed to. Water will get through the seal and run out behind the door card, over the cill and into the footwells. Mk6's have the same arrangement, so it could be the same problem.
With the door open, run a hose down the outside of the window. Water will pass the outer window scraper and into the door, but it should drain out through holes in the bottom and run over the outer cill. Make sure it is running from the drain holes and not out from behind the door card.
You can replace the seal, or for a simple fix, take off the door car, slacken off the panels retaining bolts, squirt in a bead of silicone round the bottom half on the panel and re-tighten the bolts and re-fit the door card.