Well, finding out where the water is coming from would be where I would start. I'd clean out my hinge pockets of any leaves and debris, inspect the inner wheel well (remove the plastic inner fender) and check the footwell for any other signs of water. Visual inspection of everything, then maybe pouring some water in those areas to make sure its draining properly. Check the windshield and sunroof while you're at it (even if they aren't the likely sources of this rust).
Wire wheel back the undercoating to expose the metal, you'll find out whether its simply surface corrosion or if there's been metal loss. Cut out any rust back to solid metal, weld in new metal (primed with weld thru primer), paint, remove old body grommets nearby, spray cavity wax in the rocker panel, replace body grommets and replace undercoating in that area.
It is a bit of work, but it won't ever happen again if you're thorough.
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