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Okay, so here is my story of the infamous water on the rear floorboard, discovery, research, repair and everything in between. I hope this helps someone out.

I recently purchased a used 2008 STS V6. Great deal on it since it had a rebuilt title. (Normally I would steer clear of a car like that but the owner who wrecked it had it rebuilt and then drove it for another 3 years after that.) Anyway, it had 52,000 miles on it. Showed no signs of having been in a flood so I was good to go. I did notice a bit moisture on the floors but I chalked it up to the dealer cleaning the carpets. Inside the car smelled brand new. Well. 3 days after I brought it home we had one of those rainstorms that NC is known for. Torrential rain, ALL DAY! After this monsoon I heard water sloshing about in my car when accelerating, stopping or turning. I decided to pop up the back seat and investigate. There was no water under the seat but there was under the back carpet. A LOT OF IT! I got online and looked up where this could be coming from. I also did more research about flooded cars. After many forums and info videos and such I found out about the sunroof drain holes and also determined that my car did NOT appear to be a flooded car. (WHEW!!) I quickly got to work getting the drain holes unclogged. Problem is there didn't seem to be a clog in the drains, plus there was no water in the trunk where the rear drain lines connect to the gaskets. Also, there were no water spots or stains on any of the pillars nor the headliner as is said to be common in this case. (HHMMMM?) I also got to work removing the carpets and drying everything out. During this process a neighbor of mine who is a retired mechanic came over to talk to me about what I was doing. He tipped me off to a drain at the back of the engine compartment where water flows down from the windshield. We did some water testing and such and got water draining under the car. At least a bit of it anyway. He said he would do some research and let me know. Later he told me to check under the dash for the front drain hoses of the sunroof. The next day I did just that and found that the front drain tubes are not only intact but based on their location it was not possible for those to leak onto the floor board. While under the dash I noticed the housing for the heat/ac fan against the firewall right behind where the windshield drain is. I did some more digging (literally) around that drain, removing the battery and it's housing. Behind that I found that the cabin air filter had fallen loose and there was also a fist sized glob leaves, small twigs and pine needles that had accumulated over the years. It was practically blocking the drain hole entirely. This caused the water to rise up enough during the torrential downpour to overflow into the cabin and onto the floorboard pretty much unnoticed. And since the back floorboard is the lowest point that is where it settled. Now the filter is replaces the hole is unclogged and the carpets are dried out and back in the car. I feel I should not have any more water problems for quite some time. ALSO during this process and being able see the entire metal floorboard I can safely say that there was not flood damage to my car other that the overflowing drain issue.

Sorry for the lengthy story but I do hope it helps someone out who has a similar problem.
 

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Also check the gasket at the bottom of that rear door . I had the same issue with water and the weep/drain holes in the door gasket get clogged with dirt and/or dust.
 
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