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Rain Water Leaking In (2000 Lexus ES300)

Hi folks,

I have a 2000 Lexus ES300 and I’ve had water pooling on the floor on the driver’s side, both in the front and in the back. The carpet in both areas is soaked. It’s happened twice after very heavy rainfall. There was previously a similar issue with the passenger’s side, which was addressed at the time by using silicone caulk along the base of the windshield on that side to improve the seal. I wasn’t the one who did that fix, so I’m not sure whether anything else was tried at the time, so as far as I know, that resolved the issue.

I noticed a gap in the black rubber sealing on the driver’s side and, beneath that, in/around the hood, a bunch of muddy buildup. I’ve scraped that clean and was thinking it would be worth caulking the windshield in that area.

But I’m not sure whether that’s where the leak is happening. I also understand that if the sunroof drain tubes get clogged, this can occur. I went to examine the drain holes up on the sunroof and for the life of me I couldn’t find them. I’m also not sure where the drain tubes lead out to. I’ve stuck a small pipe cleaner in every hole along the bottom of the door and the edge of the body on the driver’s side, but those all seem to lead to hollow areas in the frame, not any tubing.

So, question #1 is whether it’s possible the initial solution of clearing out the mud buildup and caulking the windshield will work. Is it possible that the buildup of mud and leaves clogged some draining that would have gone out through the hood or wheel well and sent it back into the doors and somehow into the car? Could the lack of a proper seal around the windshield have contributed?

Question #2 is where the heck I find the both the openings to the drains on the sunroof and the bottom where they drain out. And, is this more likely to be the real issue?

Question #3 is, is there another possible reason for this?

Some relevant info for diagnosis:

The carpet only seems to be particularly wet in the flat bottom part of the floor. Areas that are ridged/raised up (like under the seat, behind the pedals, etc.) seem to have remained mostly/completely dry.

Also, my speakers have stopped working the day after the most recent storm. When I turn on the radio, I hear a small clicking noise, but no audio from the speakers. Makes me think some wires got wet somewhere. But if that helps anyone figure out where the water is, I assume it could help diagnose the problem. (Also, is there any hope that whatever electrical component that got wet will just dry out and work again?)

Thanks for reading the long post, and thanks in advance for your help!

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Your numbers 1 and 2 are the most likely leak locations and where you should start to look. If its not there, make sure the drains at the bottom of the doors aren’t clogged. You can see the drains if you open the door and crawl under there enough you can look up at the bottom of the door. You’ll see a bevy of drain holes. Make sure they are open, as that’s how water that gets inside the door past the feeble window seal drains back out so it doesn’t go into the passenger compartment. Another place water gets in on sedans is the rear tail-light area. Pop the trunk lid and make sure the tail lights are well sealed where they meet up with the metal body. If you have a spare tire well in the trunk area, check to see if it has any water in it. Water can also leak in through the air vents under the windshield. There’s a water separator somewhere in the air path that should prevent that from happening and drain any rain water in the air vent path out to the ground, but it can get clogged up with debris. And the AC system drain vent can clog up and cause water to soak the carpets, but that’s usually on the passenger side.

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The water might be entering the vehicle from clogged drain tubes in the windshield wiper linkage trough.

Below the windshield, under the vent cowl cover, is a trough where the windshield wiper linkage resides.

If the drain tubes are plugged, the water collects in the trough until it finds a way into the interior of the vehicle.

This sometimes occurs because the body sealant separates from the body seam, or because the trough has a rust hole.


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Don’t forget the firewall grommets.

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Plugged sunroof drains can cause water on the passenger or driver’s floor mats. I’d start with the suggestions above, but I have done stories on Toyota products that related directly to your problem description. Here is the first Youtube video I found on how to clean the drains. I’ve had the drains in my 1990s Honda Civic and also a 2000s Subaru Legacy cause wetness on my floors. I remember the manual in one of them showed the drain exit. They usually are located just behind the front wheel wells under the car’s body. The video shows water coming out of one. Most of the sunroofs have the drain at the forward section of the sunroof and the water drains down the A-pillar. The drain tube is usually clear plastic and I could see it in my Civic. In the case of my Civic, the drain was not plugged, but somehow became mis-routed and was pointing at the floor when I found it.

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That’s an informative vdo @gorehamj , thanks for posting.

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