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Thread: E39 Touring water leak at bottom of hatch window

  1. #1
    Join Date
    Feb 2007
    Location
    Monterey, CA, USA
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    205
    My Cars
    03 525iT, 03 996C4S

    E39 Touring water leak at bottom of hatch window

    Hi all, been a long time.

    I got an SLS error in mid December, which freaked me out because ever since I replaced the air bags I now know how that system works and notice the compression running most mornings. It sounds expensive so I hate to hear it run. Thought it was finally tired and needing an expensive replacement.

    BUT...it turned out the spare tire well had about four cups of water in it, which was shorting out the compressor, or some other issue causing it to freak out. After wet-vacuuming the water out, the compressor works fine. But I can't make the leak stop. We have had very little rain in CA the last couple of winters, so I have no long it's been like this. Little paint bubbles in there, but nothing close to structural.

    I noticed water seeming to drain out of the red rear warning light in the interior panel. I pulled plastic side trim parts and the main rear interior panel. The sound insulation had clearly gotten wet many times, so I ordered a replacement ($50). Then I pulled the weatherstrips on both the tailgate and the window. Cleaned out lots of debris. Zero rust. The half rubber trim parts at the top of the bumper broke in my hands. Center section looked OK but I ordered all three for $80. Cleaned the weatherstrips really well, they looked it good shape. It was a little tricky to get the window weatherstrip back in because I had to work the edge under the "Exterior lower trunk lid trim panel" but it seemed OK. I pried at the end of that exterior trim panel (PN
    51 49 8 204 238
    ) but it seems held down with foam double stick tape, so I left it alone. Now I wonder if water is getting in under this trim piece? #9 in https://www.realoem.com/bmw/enUS/sho...diagId=51_2407

    If I crawl inside the car and a friend sprays water moving slowly upward, suddenly water pours in behind the window lock mechanism. Other areas likely were also slow leaks (debris, taillight seals which I ordered also) but this was the main culprit. I tightened the striker on the window two rotations (720 degrees) to get it to pull the window tighter against the window trim. Didn't make much of a difference.

    Any ideas? If I remove the window trim to see if water gets in underneath it, will I destroy it? It costs $145. Is it possible to reinstall the weatherstripping while leaving this trim piece in place and working the weatherstripping back in with plastic prying tools? (that's how I did it)

    I have not yet installed any of the new parts but they aren't anywhere near the source of the leak.

    To be clear, the source of the leak is between the rear wiper and the BMW roundel. a direct shot from the hose gets a steady stream of water running down what would be behind the plastic interior panel and sound proofing foam. We're careful not to spray at the wiper itself, so I don't think water is getting in that way, even though it looks that way from inside the car.

    Thanks!
    Eric Lee
    Monterey, CA
    91 M5 - sold
    97 M3 - sold
    04 V70R - sold
    03 525iT
    03 Carrera 4S
    19 Accord 2.0T 6MT

  2. #2
    Join Date
    Nov 2016
    Location
    NY
    Posts
    2,676
    My Cars
    750IL/540iT/R53/E46Vert
    I have a 99 540iT, and the same type of issue. As I am in New York, I won’t be spraying water around for a while, but I’ll see if anything else comes up, as I look around. How long have you had this car, and was there a time you knew that it did not leak?

  3. #3
    Join Date
    Dec 2016
    Location
    Canton, Ohio
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    617
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    97 528i
    laguna - any bodywork in it's past..????

    I had the same issue with mine (spare tire well was a German mobile Coy pond....) which is how I wound up owning the car. The guys at the shop said they found a plug that was left out during body repairs to the tail end of the vehicle. IIRC that plug was either under the back edge of the headliner or at the top portion of the hatch, under the interior trim on the hatch sheetmetal....(like maybe under part #5 in that diagram ????).

    I honestly don't know, but replacing that little plug fixed the issue. I did knock out one of the plugs in the spare tire well floor to ensure I didn't have anymore issues, but I never had water intrusion again regardless.
    "two wrongs don't make a right...only three lefts do...."
    '79 Euro 635csi - gone and regretting it...
    '89 gsxr-750 - former traffic knife
    '97 528i sedan - holding on strong...(just sold after 16 years of ownership - sad day)
    '03 Euro 525it - something about a famous dolphin.....

    '06 Mercury Grand Marquis (don't ask....it gets the job done....)
    '84 Specialized Allez - full Campagnolo Super Record
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    "Stinky" - Kona Stinky Five
    '86 528e
    2008 E70 X5 3.0


  4. #4
    Join Date
    Oct 2016
    Location
    Atlanta
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    2001 540iT
    I am following this!

    Sent from my SM-G970U using Tapatalk

  5. #5
    Join Date
    Feb 2007
    Location
    Monterey, CA, USA
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    03 525iT, 03 996C4S
    Quote Originally Posted by adm750 View Post
    laguna - any bodywork in it's past..????

    I had the same issue with mine (spare tire well was a German mobile Coy pond....) which is how I wound up owning the car. The guys at the shop said they found a plug that was left out during body repairs to the tail end of the vehicle. IIRC that plug was either under the back edge of the headliner or at the top portion of the hatch, under the interior trim on the hatch sheetmetal....(like maybe under part #5 in that diagram ????).

    I honestly don't know, but replacing that little plug fixed the issue. I did knock out one of the plugs in the spare tire well floor to ensure I didn't have anymore issues, but I never had water intrusion again regardless.
    I thought about removing the plug, but doesn't that let water in when driving on wet roads? I guess the water drains out after you stop.

    Some signs of body work on the right rear fender. The fender looks perfect, but a few scratches on the door end at the fender, so my guess is the fender was repaired. I could also see spot weld marks inside the door when I replaced the window regulator. I can tell the interior panel and tailgate side trim parts were removed from broken snap, etc. I've owned it for about 8 years since 93k miles, now has 213k miles.
    Eric Lee
    Monterey, CA
    91 M5 - sold
    97 M3 - sold
    04 V70R - sold
    03 525iT
    03 Carrera 4S
    19 Accord 2.0T 6MT

  6. #6
    Join Date
    Nov 2016
    Location
    NY
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    2,676
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    750IL/540iT/R53/E46Vert
    Try using painters tape in that channel to see if you can narrow down the leak.

  7. #7
    Join Date
    Dec 2016
    Location
    Canton, Ohio
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    97 528i
    Quote Originally Posted by lagunae34m5 View Post
    I thought about removing the plug, but doesn't that let water in when driving on wet roads? I guess the water drains out after you stop.
    In Ohio is rains quite a bit, not to mention the shit salt/brine water we drive through in the winter. Never had an issue with any significant amount of water getting in the well with the plug out. Some moisture (nothing standing...) and typical residue around the edges of the hole from the salt and crap, but I coated that opening with some undercoat spray and it never affected anything.

    hope you find the cause....

  8. #8
    Join Date
    Jun 2012
    Location
    Mundelein, IL
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    837
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    840Ci/6 528iT Europa TCS
    I had a pesky leak in my wagon. The cloth type panel between the battery and one the fuse boxes was always wet. Then the rear floor carpet was wet. I checked the drains for the sunroof but they were clear. I finally removed the little GPS antenna at the exterior rear end of the roof. The grommet around the GPS antenna that seals it to the body was pretty dried out. I removed the antenna and put a rubber grommet/plug where the antenna was and everything is dry now. This may not be your problem but it still may be worth looking at.

  9. #9
    Join Date
    Dec 2006
    Location
    West of Boston, MA
    Posts
    726
    My Cars
    2001 BMW 540iT/6

    E39 Touring water leak at bottom of hatch window

    Quote Originally Posted by rjbaren View Post
    I had a pesky leak in my wagon. The cloth type panel between the battery and one the fuse boxes was always wet. Then the rear floor carpet was wet. I checked the drains for the sunroof but they were clear. I finally removed the little GPS antenna at the exterior rear end of the roof. The grommet around the GPS antenna that seals it to the body was pretty dried out. I removed the antenna and put a rubber grommet/plug where the antenna was and everything is dry now. This may not be your problem but it still may be worth looking at.
    +1. You need a doorman transmission plug, but same here.

    I do have wet license plate bulb housings… gonna replace the whole handle area when I eventually do paint.


    Sent from my iPhone using Tapatalk
    Last edited by scottieducati; 01-17-2022 at 03:40 PM.

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