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E39 (1997 - 2003)
The BMW 5-Series (E39 chassis) was introduced in the United States as a 1997 model year car and lasted until the 2004 when the E60 chassis was released. The United States saw several variations including the 525i, 528i, 530i and 540i. -- View the E39 Wiki

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Old 10-07-2011, 09:47 AM
komato3 komato3 is offline
Registered User
Location: River Edge, NJ
Join Date: Feb 2009
Posts: 28
Mein Auto: 2002 525iT
e39 2002 Water inside cabin, sunroof drain fix, pics

Hi everyone

Joining the club of those who got water in the cabin!
It started out of a sudden during a heavy rain, I opened the door of my 2002 E39 525IT and saw literally a puddle of water on the rubber mat. Maybe a liter or so.. Water trickled down from under dash a bit to the right from brake pedal.. I was shocked as Iíve never seen such a miracle before.. Itís a scary thing not only because of the wet panels, mold and smell but also that you never know if and when water gets inside your carís electronics and may cause fire.. So I needed to understand the cause to avoid it in the future.
I learned from forum you fellow comrades that the culprit #1 is sunroof drain.. But I needed to see how it's happening.. such a guy i am..
I slid the sunroof back and poured a fair amount of water (half a cup) right into the driver side corner of the sunroof cassette.. I got water immediately inside the cabin down A-pillar around hood release handle. Problem confirmed, good.
I removed visor and overhead handle and all the obvious stuff to be able to pull down the headliner and to look inside.

First step Ė important! I detached the rubber drain tubing. I noticed that itís very soft, easy to squeeze and that the clips that hold the tubing DO squeeze it in several points causing bottleneck clogging spots Ė which is no good to designers.
I blown into the tube Ė as stupid as it sounds and felt the following: at the very first moment there was resistance to the air I blew into the tube and then Ė sudden release and gurgling sound on the other end. So not being an idiot I quickly pointed the tube to outside of the car and right away there came down quite a bit of water out of it.. Seemed like there was a clog in the tube.. But I wasnít sure and continued with my investigation

I poured some water into the same corner again and looked from underneath what happens to the drain tube.. Some water came out through the drain tube as it was supposed to but some water trickled from the corner marked the red arrow .
Observation: the drain tube (marked with blue arrow) was quite easy to remove, so I would consider to secure it with a hose clamp or at least with a plastic cabletie.

By the way, my sunroof stops sliding backwards at this position and doesnít go any further. Is it how itís supposed to be? When I attempted to release the headliner I couldnít remove the frame as there were 6 screws on the back under the sunroof lid. Any ideas?

Thatís how driverís corner of the sunroof cassette looks like. Except I removed the stop piece and placed its screw back to plug the hole. Red arrow Ė drain hole.

Another view just to make sure the drain hole is clearly seen..

Important thing Ė I found a small square piece of soft sealing material and after some more test I finally figured out what actually happened. That piece fell out from the spot marked with red arrow and clogged the drain tubing at a nearest pinch point. I plugged the tube and carefully poured water into the corner Ė water reached the level shown with two blue dashed lines Ė nothing leaked, but once water got to the red arrow spot it went down into the carís interior immediately.
So thatís how clogged drain tubing cause leaking inside the car.

A closer look at the culprit

So what Iím gonna do Ė seal the circled area with silicone caulk and also seal red arrow spots just in case..

Iím pretty sure itís going to heal the problem
Good lesson to myself Ė from time to time test the drains, blowing into them through a piece of tubing

Hope my experience helps
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Old 10-07-2011, 10:03 AM
bluebee's Avatar
bluebee bluebee is offline
Seek to understand,^Value
Location: San Jose, California
Join Date: Mar 2008
Posts: 25,236
Mein Auto: 02 BMW 525i M54 auto 130K

I'll add this to the bestlinks:
- How to repair & reset the sunroof (1) (2) (3) & how to fix sun roof rattles (1) & how to test & fix moonroof leaks (1) (2) (3) (4) (5) (6) causing water on the front passenger carpet & how to remove the roof headliner (1) & how to free up a stuck open sunroof (1) (2) & how to replace broken moonroof sunroof glass (1)
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Old 01-02-2012, 05:24 PM
Jobu Jobu is offline
Location: Northeast, NJ
Join Date: May 2007
Posts: 26
Mein Auto: 2003 530i, 2011 X5d
Thanks for the post. It helped me as i was freaking out, trying to solve my version of this problem!

At least the car starts now. I haven't totally diagnosed the problem yet., but due to this and other posts, I'm on well my way!
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Old 06-06-2015, 10:08 AM
EdwardP EdwardP is offline
Registered User
Location: Puerto Rico
Join Date: Jun 2015
Posts: 1
Mein Auto: 2012 X5 2004 330ZHP
Question Same leak issue on E39

I know this in an old post but I was wondering if you are still out there. Did you or any other member has fixed the problem with the drain unclogging and sealing those marked areas with silicone?. Before reading your post I found out the exact same condition in my e39 sunroof. Just want to know the outcome before putting all my pieces back together.

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