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Re: Water on floorboard caused by heavy rain. possible...
The plastic cowl that goes between the windshield and the air intake inlet for the cabin blower motor needs a seal added to it. Go to a hardware store and get a thin 3/16" thick or less weatherstripping seal and place this on the plastic cowl piece. There might already be some there from the factory but it is most likely hard and cracked. This will keep the majority of the water from running into the air intake box. Also there is suppose to be a rubber seal on the edge of the sheetmetal just above the air intake. Make sure that weatherstripping piece is in place and not torn in any way.
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If you have a sunroof it could be the drain that follows the front pillar letting out under the front fender. These hoses are known to plug and crack open releasing water into the floorboards.
Driver side door check along top and front edge for tears or twisted looses sections. Internal to the door water can drain down along the window and is released outside the door seal. If the bottom of the door has the opening that releases the water plugged then water will drain over into the floorboard.
Most water leaks come from around the windshield area. Has the windshield been replaces recently? If so it may not be sealed properly. Another area where water may penetrate is through the cowling area under the wiper blades/arm where fresh air enters the car. There are water drains under this cowling allowing water to drain and if they are plugged with leaves/debris, water will enter the vehicle. Is the vehicle rusted around the windshield area? If so, suspect this to be the source of water intrusion. Most glass/windshield repair companies will diagnose water intrusion problems
several qs. What year make and model is the car? Is car level when water fills floor? Does it always happen every time it rains fairly heavily? Is the trunk always dry? Talk to other owners for their experience.
I had the exact same problem with my 1995 neon. It was leaking around the tail light. I pulled the tail lights off and put a heavy coat of RTV silicone on the gasket, and 2 years later never happened again
a couple things to look at if it has a sunroof the sun roof would have drain hoses that run down in each corner next you need to look at the cowl this is the section in front of the windshield that has a drain on it as well if you find nothing there the next step would be to remove the seats and carpet and sit in the car while running water over it either way you should remove the carpet and make sure it is dry all the way threw or mold will start to grow and you will never get ride of it not good for your heath other key spots to look at is if the windshield was ever replaced it could be a poor seal
Most floor leaks that show up after sitting in the heavy rain are leaking windshields...have you had your windshield replaced before? (The windshield installation should be under warranty...at least 1 year:) If you are driving and the floorboard is filling up...the floorboard itself must have a hole or plug missing...The VW usually has floor drain plugs located under the carpet...from your description, the windshield is probably the cause...are there any window trim pieces missing? This is an annoying problem...you can also test the windshield by having someone run a garden hose on the outside while you look inside for the penetration spot or spots...Hope this helps. A glass shop might do a free inspection...