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Cars are equipped with drain holes designed to release channeled water runoff. Water seeps into the gap at the base of windows between glass and door panels when the car is washed and during rainstorms. As long as drain holes are kept clear and open, standing water will not accumulate. However, if drains become clogged up with dirt or other debris, water will be trapped at the base of doors to start the rusting process. (reference)
An aggravation of the problem in this specific area is due to the lap seams between the inner and outer door skins where moisture from condensation or standing water will accumulate. Some designs actually form a groove at the top of the seam where water sits for long periods of time. These seams are on a vertical axis and below the drain holes, making them damp and so rust prone. This same vertical, water holding seam is in most trunk lids and engine hoods. Volkswagen had a horizontal door seam that drained throughout it's entire length in the 70's, but reverted to the non-drain, vertical model with the Golf and all subsequent models.
