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Thread: E39 Touring Hatch Window Full of Water

  1. #1
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    '99 528iTA Sport

    E39 Touring Hatch Window Full of Water

    I've been trying to diagnose a water leak that I'm seeing on the rear left corner of my headliner. I dropped the headliner down a little bit so check the sunroof drains, and fortunately they don't seem to be leaking. I also resealed the weather stripping with some 3M black weather strip adhesive, and that didn't make any difference.
    I'm realizing that the problem is likely the fact that my window is full of water. I know it's not uncommon on these cars, but has anybody found a fix for it? I'd like to keep water out of my trunk area.
    I already pulled the plugs on the bottom of the window and cleared it out, and that isn't even letting out water at this point. But I certainly hear it sloshing around every time I open the window.

    Does anybody have any idea on what to do about this?
    1999 528iT Sport- 2/1999 Alpine White/Sandbeige
    2003 X5 3.0i Stahlgrau/Gray
    2001 330Ci Topazblau/Black
    1984 318i Balticblau/Black
    1995 525i Hellrot/Beige (brother's)
    2007 335i/6 Titansilber/Black (brother's)
    2004 X3 2.5i Titansilber/Gray M54B30 swapped (dad's) (Sold)
    2006 330i Alpine White/Black (Sold)
    ...and some Volvos and other stuff

  2. #2
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    So, when you open the hatch window, you hear water sloshing? Any rust in the hatch itself?

  3. #3
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    Quote Originally Posted by CPHES View Post
    So, when you open the hatch window, you hear water sloshing? Any rust in the hatch itself?

    Yes, I hear the water rush to the top of the window when I open it. No rust to be found anywhere.
    1999 528iT Sport- 2/1999 Alpine White/Sandbeige
    2003 X5 3.0i Stahlgrau/Gray
    2001 330Ci Topazblau/Black
    1984 318i Balticblau/Black
    1995 525i Hellrot/Beige (brother's)
    2007 335i/6 Titansilber/Black (brother's)
    2004 X3 2.5i Titansilber/Gray M54B30 swapped (dad's) (Sold)
    2006 330i Alpine White/Black (Sold)
    ...and some Volvos and other stuff

  4. #4
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    Quote Originally Posted by bmdubya1198 View Post
    Yes, I hear the water rush to the top of the window when I open it. No rust to be found anywhere.
    To be clear. When you open the whole hatch you hear water run to the lowest spot as the hatch lifts up? That water would have been near the bumper when the hatch was closed and after raising the hatch is near the back of the roof where the hinges on the hatch are located?

    If I'm reading this right, opening just the rear window would have no effect - you wouldn't hear any water move.

    So the question is how is the water getting into the rear hatch between the outside sheet metal and the inside vapor barriers or interior trim?

  5. #5
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    There appears to be a mis communication. The hatch is 2 pieces. The gate which is the body and it latches to the body of the car. Then there is the glass, which mounts to the gate. Where is the water filling - in the glass part ( I’ve see it come down thru the third brake light housing - or in the base of the hatch?

  6. #6
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    No, the water is within the window itself. When I move the hatch separately from the window, I can't hear/feel water in the tailgate. I hear it rush from the top to the bottom though when I move the glass.
    1999 528iT Sport- 2/1999 Alpine White/Sandbeige
    2003 X5 3.0i Stahlgrau/Gray
    2001 330Ci Topazblau/Black
    1984 318i Balticblau/Black
    1995 525i Hellrot/Beige (brother's)
    2007 335i/6 Titansilber/Black (brother's)
    2004 X3 2.5i Titansilber/Gray M54B30 swapped (dad's) (Sold)
    2006 330i Alpine White/Black (Sold)
    ...and some Volvos and other stuff

  7. #7
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    2001 BMW 540iT/6

    E39 Touring Hatch Window Full of Water

    Quote Originally Posted by bmdubya1198 View Post
    No, the water is within the window itself. When I move the hatch separately from the window, I can't hear/feel water in the tailgate. I hear it rush from the top to the bottom though when I move the glass.
    Wut….

    I don’t understand how that’s possible… are you sure it’s not the pistons making a noise??

    Potential leak sources in the rear are:

    Rear center tail light
    FM antenna on top of the roof
    Outer tail light housing (too low and far from window to be your problem)

    I’m not aware of others…


    Sent from my iPhone using Tapatalk

  8. #8
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    Yep, in all the years I have owned E39 wagons, never seen this issue in any of my cars, or any body else’s. Now, thinking about this, how could water get in there….. Well, here’s a question, does your glass hatch have all the trims in place? If so, carefully pull the black trim piece that runs across the top section. There are rubber boots that’s supposed to keep water out, there are two of them with the wiring harnesses that go into the glass hatch, one is for the defroster lines, and the other is for the third brake light. If those harness boots are not on properly, or all shredded up from age, maybe water got in there that way? But I’m gonna warn you now, pulling of the black trim cowling, the tabs are definitely gonna break off. You will just have to figure out a way to get it back on. I made tabs out of brass, bent in 90 degrees, folded over, bent 90 degrees on the other end, epoxied to the cowling exactly where the old tabs were. The other pain in the butt part was fishing the old broken tabs out of the metal pinch clamps that are embedded into the plastic receptacles. A pain, but doable.
    Set the controls for the heart of the sun

  9. #9
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    Took a couple pictures of the glass. Water must be behind those interior black trim pieces. Maybe it leaks where the wiper is attached?

    Sent from my SM-G970U using Tapatalk

  10. #10
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    Ah, the wiper may be an entry point.
    And yes, I know it sounds crazy, and I have no idea where else water could even get in, but the water is in fact in the glass. There are two little plastic plugs on the bottom of the glass, and when I pulled one and tilted the glass down, I was able to drain some water from there. I lost the plug, so it should drain right out, but it seems the water doesn't get to that point to actually drain.

    It's definitely not the shocks, I replaced those last year, and the problem existed before and after that.

    The part around the glass that I circled is where the water is accumulating.
    Screenshot 2022-05-17 110730.jpg
    1999 528iT Sport- 2/1999 Alpine White/Sandbeige
    2003 X5 3.0i Stahlgrau/Gray
    2001 330Ci Topazblau/Black
    1984 318i Balticblau/Black
    1995 525i Hellrot/Beige (brother's)
    2007 335i/6 Titansilber/Black (brother's)
    2004 X3 2.5i Titansilber/Gray M54B30 swapped (dad's) (Sold)
    2006 330i Alpine White/Black (Sold)
    ...and some Volvos and other stuff

  11. #11
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    Well now that makes sense. I've never touched those trim pieces but I am sure they will break if you do! Then you'll just have a leak...

    Sent from my SM-G970U using Tapatalk

  12. #12
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    That area you marked is the frame. The glass is urethaned to it. Did you even read my post? The only area where water can make it in, when the glass hatch is closed, are those rubber boots up in the top of the frame.
    Set the controls for the heart of the sun

  13. #13
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    Quote Originally Posted by BimmrMeUpSnotty View Post
    That area you marked is the frame. The glass is urethaned to it. Did you even read my post? The only area where water can make it in, when the glass hatch is closed, are those rubber boots up in the top of the frame.
    Yes, I'm aware. I need to double check the boots, but I don't remember them being damaged. I will take a look at this today.
    1999 528iT Sport- 2/1999 Alpine White/Sandbeige
    2003 X5 3.0i Stahlgrau/Gray
    2001 330Ci Topazblau/Black
    1984 318i Balticblau/Black
    1995 525i Hellrot/Beige (brother's)
    2007 335i/6 Titansilber/Black (brother's)
    2004 X3 2.5i Titansilber/Gray M54B30 swapped (dad's) (Sold)
    2006 330i Alpine White/Black (Sold)
    ...and some Volvos and other stuff

  14. #14
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    Quote Originally Posted by BimmrMeUpSnotty View Post
    That area you marked is the frame. The glass is urethaned to it. Did you even read my post? The only area where water can make it in, when the glass hatch is closed, are those rubber boots up in the top of the frame.
    Are the boots under the trim pieces that cover the hinges? Been a while since I had them off.

    Sent from my SM-G970U using Tapatalk

  15. #15
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    Quote Originally Posted by rlordjr View Post
    Are the boots under the trim pieces that cover the hinges? Been a while since I had them off.

    Sent from my SM-G970U using Tapatalk
    No, not the hinges, the big trim piece that cuts across the top, you have to pry them off the tabs, and it doesn’t matter if you pry in the right spot, those tabs will break off. Everything is brittle, unless you replaced that piece not long ago. There are two rubber harness shrouds that route the wires into the frame, which is full of water, according to OP. I’m betting, either the boots are torn, or had been pulled out, and not placed back on properly, and water is getting past the plastic trim cover, ans finding its way into the frame at high speed in the rain. It’s the only way I can imagine water is finding it’s way in.
    Set the controls for the heart of the sun

  16. #16
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    I pulled off the plastic cover (it was already held in with double sided tape, it had broken several years ago) and the boots are in good condition and properly seated. I pulled apart the third brake light and the trim cover behind the rear wiper. No evidence of water entry and no damaged seals that I can find, but I can definitely hear the water when I move the glass. Maybe the seal around the glass is letting water in at some point.
    1999 528iT Sport- 2/1999 Alpine White/Sandbeige
    2003 X5 3.0i Stahlgrau/Gray
    2001 330Ci Topazblau/Black
    1984 318i Balticblau/Black
    1995 525i Hellrot/Beige (brother's)
    2007 335i/6 Titansilber/Black (brother's)
    2004 X3 2.5i Titansilber/Gray M54B30 swapped (dad's) (Sold)
    2006 330i Alpine White/Black (Sold)
    ...and some Volvos and other stuff

  17. #17
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    Well how about making up a water sucker with your shopvac, duct tape and a long piece of small plastic tubing? Stick it in the frame via where the boots are and maybe you could at least remove the water. If the boots are good then I guess you should check the urethane seals between the glass and the frame. I think you should take the glass off the car if you haven't already and work on it that way.

  18. #18
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    Hmmm, I just don’t see how that water got in there. Yep, like rlordjr says, maybe pull the rubber boots loose, duct tape the shopvac hose as good as possible, with the hatch open, the water should flow to that spot near those rubber boots, leave the vacuum on.

    - - - Updated - - -

    Cut out that glass carefully! I think they go for around $400 bucks or so. Pulling the rear wiper assembly can be a test of your nerves, be ready to order a new shaft assembly, those things don’t like to come loose.
    Set the controls for the heart of the sun

  19. #19
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    Yeah, I have no idea where it could be coming in there. I'll try to put a shop vac on it, that's a good idea. I'll see if I can get any more water out of there.
    1999 528iT Sport- 2/1999 Alpine White/Sandbeige
    2003 X5 3.0i Stahlgrau/Gray
    2001 330Ci Topazblau/Black
    1984 318i Balticblau/Black
    1995 525i Hellrot/Beige (brother's)
    2007 335i/6 Titansilber/Black (brother's)
    2004 X3 2.5i Titansilber/Gray M54B30 swapped (dad's) (Sold)
    2006 330i Alpine White/Black (Sold)
    ...and some Volvos and other stuff

  20. #20
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    1999 540i Touring 6speed
    Hi
    You know that the rear glass frame is a common place for rust.
    On my Touring, I don't have active leaks (you can use a pressure washer on the car as long as you want without being able to spot any leaks)
    But when it rains for multiple days, I sometimes found a small puddle on my luggage cover. I've come to the conclusion that the rust in the bottom right corner of the glass frame (which is quite bad I have to admit) was letting humidity creep-in and when it was trying to evaporate, it was condensing INSIDE the top of the frame, and when it became liquid again, was dripping from my third break light . I have just bought a new rear glass assembly (frame+glass+rear wiper) from a guy who bought the frame new from BMW recently, but never had the opportunity to mount it on the car.
    1999 540i Touring 6speed M62TU

  21. #21
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    I've looked a little more, and I can't find anywhere that the water could be coming in. I'm going to reseal the top left corner of the hatch weatherstripping to try to keep water from getting onto the headliner, which is the main issue. Obviously that doesn't take care of the window though.
    1999 528iT Sport- 2/1999 Alpine White/Sandbeige
    2003 X5 3.0i Stahlgrau/Gray
    2001 330Ci Topazblau/Black
    1984 318i Balticblau/Black
    1995 525i Hellrot/Beige (brother's)
    2007 335i/6 Titansilber/Black (brother's)
    2004 X3 2.5i Titansilber/Gray M54B30 swapped (dad's) (Sold)
    2006 330i Alpine White/Black (Sold)
    ...and some Volvos and other stuff

  22. #22
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    I was thinking of this, you need to get that water out, and keep it out. I was thinking, if you do get it dry in there, and water gets back in, might be a good idea to drill a 1/8th” hole at both bottom corners, maybe one in, or near the middle. Go slow as to keep shavings drawn out with the drill bit, then with a small brush, apply POR15 into the hole, and the new exposed metal to keep it from rusting. Pull the rubber boots loose up top, clean them with silicone real well, inside and out, clean the open ports while the boots are off, get them back on properly, the only other way in for water would be through the wiper shaft, and that is a bear to pull off, chances are, you will have to break it, and replace it with new.

    - - - Updated - - -

    One more thing, check the hinge points, maybe a bolt is missing, and water could be coming in that way?
    Set the controls for the heart of the sun

  23. #23
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    I'll have to give it a look and try to get any water out of there. I resealed the weatherstripping earlier this afternoon, so hopefully that will finally keep water out of the car. Now to keep it out of the window and tailgate.
    1999 528iT Sport- 2/1999 Alpine White/Sandbeige
    2003 X5 3.0i Stahlgrau/Gray
    2001 330Ci Topazblau/Black
    1984 318i Balticblau/Black
    1995 525i Hellrot/Beige (brother's)
    2007 335i/6 Titansilber/Black (brother's)
    2004 X3 2.5i Titansilber/Gray M54B30 swapped (dad's) (Sold)
    2006 330i Alpine White/Black (Sold)
    ...and some Volvos and other stuff

  24. #24
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    Alright, an update. We got an absolute monsoon earlier, and I noticed a puddle on my trunk mat. I got in from the rear seat to check the leak so I didn't get water everywhere by opening the tailgate, and sure enough, it's coming from the middle brake light. Dripping right down. I'm assuming that's also where it's getting into the window itself.
    Fortunately though, there isn't any water on the headliner this time.
    1999 528iT Sport- 2/1999 Alpine White/Sandbeige
    2003 X5 3.0i Stahlgrau/Gray
    2001 330Ci Topazblau/Black
    1984 318i Balticblau/Black
    1995 525i Hellrot/Beige (brother's)
    2007 335i/6 Titansilber/Black (brother's)
    2004 X3 2.5i Titansilber/Gray M54B30 swapped (dad's) (Sold)
    2006 330i Alpine White/Black (Sold)
    ...and some Volvos and other stuff

  25. #25
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    97 528i
    The window frame may be a "wet area" just the the inside of a door so getting a bit of water in there shouldn't be an issue.

    If water is getting in the frame of the window glass, regardless of how it is getting in there, it should drain out the little drain holes along the bottom of the frame. You can see one in your picture at the right bottom edge just before the corner. I'd check those drain holes for blockage before doing anything else...

    correct me if I'm wrong gents
    "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
    '99-ish Cannondale CAAD4
    "Stinky" - Kona Stinky Five
    '86 528e
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