I'm not sure if this is the problem you're having, but if you have a sunroof there is a common problem with the drains that run along the A-pillars in some models or the B-pillars in other models depending on the position of the sunroof. The best way that I have found to clear up drainage problems is to go to a gun store (or in some areas a sporting goods store) and purchase a gun cleaning kit look for one made specifically for long lower caliber kits like those designed for a 22 caliber rifle or air rifle. Using the longest extension & brush (it looks like a heavy duty pipe cleaner) spray a non-oily cleaner (such as brake or intake cleaner) into the drain holes on both sides of the sunroof tracks and push the rifle brush through the entire length of the tube. This is a good time to also lubricate the tracks for your sun/moon roof as well. I'd recommend using a non-sticky lubricant such as graphite which you can get at any auto parts store usually labeled keyhole or lock cylinder lubricant (the one I've seen most often is in a small blue bottle with a white top) apply the graphite liquid to the tracks & wipe off the excess, it also works very well in ignition and or door locks, on power antenna shafts & motors, power window regulators / tracks / motors, and door / tail gate / hood hinges. It's an excellent lubricant & doesn't leave a sticky or oily residue & it is less effected by cold temperatures than traditional lubes. The same process works very well in order to clearout any blockage of the drain tube from the evaporative chamber in air conditioning systems. All a/c systems have some sort of drainage tube to remove moisture that is created during the process of running your air conditioning as well as the defogger for your windshield.
Good luck with the water problem, I hope this helps, if so, please feel free to share it on any other forums you post on, and if you have suggestions to improve it please let me know as I do this kind of work on a regular basis & anything that would make it easier or that would work better would be welcome information...
-Christopher