Most likely candidate is a shrunken door seal. To fix that, just pull the seal off, then reinstall it starting at the top center and pushing all the way in, all the way around. This (due to shrinkage of the seal) will leave you with a gap at the center of the bottom under the sill. Cut a piece from a junkyard seal to patch it to prevent noise and dust if you like, but just reinstalling the seal tightly will stop the water.
Less likely is the misplacement of this piece of sound deadening asphalt. (goes to get pic...) Under rear seat: water entered through the ventilation grille and then through a 2"x3" hole in the interior metal sheet where a factory stick-on seal had come undone. Fix: peeled back the factory seal to expose the hole, cleaned off the dust and used strip caulk to re-seal the original sealing material.
Worst is rust through at the seam between the floor under seat base and the inner wheel well. :( For that, you can try cleaning it up really well, priming then applying seam sealer. But expect the rust, unless completely removed and replaced with good metal, to come back.