This is usually a symptom of the seals between the door panel and the ancilliary carriers starting to fail.
The carriers (that hold the window mechanisms, speakers & etc.) are sealed to the door outer by a closed-cell foam self-adhesive strip. This fails over time (don't know why, may just be fatigue, reaction with the glue, expansion/contraction or gremlins) and becomes porous, usually starts in the corners.
Rain runs down onto the carrier from the window. If the foam has started to leak, it gets onto the door sill and eventually some gets into the car, pooling in the footwell. Best way to check, open the doors after heavy rain. If water runs off the door sills, you've got leaky seals: it may not be in the footwell yet, but it will be.
The VW replacement strip is a mastic, which will deal with vibration and the metal expanding with heat, but probably will need renewing if you have to take the carrier off again. However it does stop your doors leaking, which is really the important thing.
Taking off the carriers completely requires some careful work with the windows. You don't have to do this, all I did was take off all the
lower bolts but leave the top bolts along the window opening in place, just loosened off a bit. I could then move the carrier out enough to remove the old foam (make sure it's all gone) and replace it with new sealer strip over the bottom and sides of the carrier, up to 2/3 of each side. If the door fills up beyond that with water, then something else is the matter