Often, water in the foot wells is down to the window regulator carrier panel seal. On all cars, water runs down the windows and some gets into the door, past the outer scraper seal. The water then drains out through drain holes in the bottom of the door and runs out over the cills to the outside. In the old days there was a plastic membrane that stopped water that was inside the door from coming into the car. These days the plastic has been replaced with a metal panel that has the window motors and other such stuff attached to. If this panels seal fails, water can seep out from behind it, run down the inside of the door and out from behind the door card, over the cill and onto the carpet.
A way to check if this is happening is to run a hosepipe down the outside of the window with the door open. Water should be seen running out through the bottom of the door, via the drain holes. If you can see any coming out from behind the door card, there's your problem.
