BMW E61 Trunk Leak Sunroof Drain Failure 2004-2010 5 Series Touring Wagon

BMW E61 Trunk Leak Repair – 4 Hours
Repair cost level 1

The BMW Repair Guide used this 2006 530xi touring for the following article.

2006 bmw 530xi touring WBANN73576CN02628

Repair Summary
This article gives detailed instructions on repairing a trunk leak due to sunroof drain failure in a BMW E61 touring wagon vehicle. Even though we used a 2006 BMW 530xi touring wagon to perform this repair, this article can be applied to any 2004-2010 5 series touring wagon with minor modifications to the repair steps.

Indications of a BMW E61 trunk leak due to a sunroof drain failure are water in the battery compartment, spare tire well, and right or left trunk storage trays.

All you have to do is spend a few minutes researching the BMW E61 5 series touring wagon in online forums to discover one unmitigated fact; the E61 is notorious for trunk leaks directly related to its panoramic sunroof drains. Many car owners are astonished to find out their vehicle sunroofs are not water tight, and if they were not drained they would soon be driving a swimming pool with wheels.

To address this issue, the panoramic sunroof on the BMW E61 was manufactured with four drains in its frame. The two in the front of the sunroof frame channel water down the A pillars and out of the vehicle behind the front wheels. The two in the rear of the frame channel water above the headliner, down the D pillars and out of the vehicle behind the rear wheels. All of this is done through a simple system of rubber pipes with valve flaps on the end. The valve flaps allow the water to exit the bottom of the car without allowing dirt and little critters to come in.

The problem that has arisen with this method of drainage is that leaves and debris can get caught in the system…most notably in the valve flaps and the frame drain holes. A good comparison to this are the gutters on your house; when the gutters and downspouts become clogged with leaves, the water overflows and pours down the side of the wall (and on your head). The same thing happens in your E61 wagon…when the system gets clogged, the frame drains overflow and dump water into the headliner. If it is the rear drains that are clogged, this water flows down the D pillars and into your battery compartment, spare tire well, and storage trays. The results of this can be catastrophic; the water can destroy electronics, short out batteries and sensors, and can ultimately leave your vehicle undriveable.

One of the main casualties in a BMW E61 trunk leak is the intelligent battery sensor (IBS). The IBS is located on the negative terminal, and manages both the “state of charge” and “state of health” of your battery. This data is continuously fed to your BMWs DME (the engine computer module), which in turn manipulates your vehicle’s electronics to conserve power. When your IBS short circuits due to a trunk leak, all hell breaks loose. Anything and everything can and will happen, from electronics randomly shutting down, to a complete vehicle “no start”. If you have a BMW E61 trunk leak and have IBS damage due to water infiltration in the battery compartment…simply unplug it. This will return your vehicle to “normal” until the leak is fixed and the IBS can be replaced. For more information on your IBS and how to replace it, please see our repair article concerning this issue. The following image shows you how to unplug the IBS so you can normally operate the e61 intelligent battery sensorunplug the IBS to continue normal operation of your vehicle

Repairing a BMW E61 trunk leak
There are many online videos, forum threads and articles on how other BMW owners have attempted to clear the blockage in the rear sunroof drains in their BMW E61 5 series touring wagons. Although we admire the ingenuity and resourcefulness of these bimmer enthusiasts, the BMW Repair Guide only recommends using what we call the “cut and splice” method to clear the sunroof drains in your E61. The BMW Repair Guide strongly discourages it’s readers from pulling the drain tubes loose from the floor pan of the vehicle, or removing the bumper and undercarriage covers to access the drain fittings. These are both unnecessary and incorrect methods of fixing clogged sunroof drain lines.
The “cut and splice” method of removing a blockage requires accessing the sunroof drain tubes in the headliner and D pillars of the car, cutting them open, cleaning the sunroof drain, clearing the valve under the vehicle, testing the system, and then replacing the upper drain hose with a wider diameter piece of clear vinyl tubing. It may sound complicated, but is actually a relatively simple operation. The best part of the “cut and splice” method is you only have to remove the “D” pillar covers and drop the rear of your headliner to thoroughly clean the entire drain system. There is no need for a complicated disassembly of your vehicle’s bumper or undercarriage.
We have learned from trial and error that this is the best way to clear the drains on your BMW E61 wagon. It also has an added benefit that other methods don’t offer; replacing the upper portion of your drain line with a larger diameter clear 1/2″ vinyl tubing allows for faster and more efficient draining of the sunroof. It also allows you to monitor for future clogs in the system and is easily disassembled for future cleaning. The BMW Repair Guide recommends cleaning and replacing both the right and left sunroof drain tubes during this repair even if one of them is not leaking.There are a few supplies that you will need to purchase prior to starting this repair. Everything except the 4mm bicycle shifter cable (used to “snake” out the lower portion of the drain tube and the valve under the car) can be purchased at your local home improvement store. The 4mm cable can be purchased on Amazon (link provided below)…or your local cycling shop.
Many BMW E61 wagons will have water damage to the headliner from the leaking sunroof, especially in the rear of the vehicle where it has been pouring out into the battery and electronics trays. This moisture tends to build up in the ceiling fabric causing it to separate from the headliner. As you can see from the following photo our fabric completely separated in the rear of the vehicle when we dropped the headliner to access the roof drains. We will show you a temporary fix for this in the following article, although ultimately you will need to get the headliner professionally recovered.fallen headliner due to leak in sunroof drains

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There are no parts needed for repairing a sunroof drain leak.

The BMW Repair Guide makes every attempt to publish their repair articles with detailed step by step photographs, videos and written instructions. Since this repair deals with varying years and models, your vehicle may be slightly different than what is shown in the following steps and images. Some repairs may also require additional steps not covered in our articles like: removing covers from the engine and undercarriage, moving wires or hoses to access parts, cleaning and lubricating parts associated with the repair and performing general maintenance.
Section 1 – BMW E61 trunk leak; preparing vehicle for repair

Before repairing your sunroof drains, it is very important that everything is removed from the trunk and all of the standing water is vacuumed out. This includes all personal items, the battery, the floor liner, and everything in the spare tire compartment.

  1. Remove the battery compartment tray on the right side of the vehicle. You can see ours was completely filled with water.BMW E61 Trunk Leak - right storage tray leak
  2. Use a 10mm socket wrench to remove the negative and positive terminals from the battery. Remove the battery clamp with a phillips screwdriver, grasp the battery and remove from its compartment.BMW E61 Trunk Leak - remove battery from vehicle
  3. Remove the trunk floor. Next, lift out the foam electronics tray and remove the air suspension and rear tailgate control modules and the three relays. If these are wet you will need to dry them with a hair dryer. Remove the spare tire from the vehicle.BMW E61 Trunk Leak - electronics tray spare tire well has water
  4. Pull the wiring harness loose from above the trunk fuse panel. Fold the protective fabric up and tuck away.BMW E61 Trunk Leak - remove the fuse box wiring harnessfold up protective fabric around fuse block
  5. Use a wet vac and a hair dryer to thoroughly remove all of the standing water from the battery compartment and the spare tire well. Use a hair dryer to dry out the trunk fuse block and the top of the battery. The goal here is to make sure everything is completely e61 trunk leak - vacuum out all standing water bmw e61 trunk leak - thoroughly dry fuses and electronics
  6. Our trunk fuse block was saturated with water. Pull out electrical connectors, relays and fuses if necessary to make sure the fuse block is thoroughly dried out with the hair dryer. If you notice any corrosion on the connectors, spray them with a good electronics cleaner like CRC Electronics e61 trunk leak - pull out electricasl connectors and dry This connector has corrosion from water infiltration


Section 2 – Diagnosing a clogged sunroof drain

It is just about guaranteed that if your battery compartment, spare tire well, and/or right and left side storage trays are filling up with water after a heavy rain, you have a clogged sunroof drain line(s) in your vehicle. If your lines are clogged, the water will overflow out of the sunroof drains and run down the top of the headliner and into the D pillars. The following is a quick test to verify this is your issue.

  1. Retract your sunroof all the way so it is completely e61 trunk leak - retract sunroof
  2. Take a full cup full of water and slowly pour it into the right side of the sunroof e61 trunk leak - pour water into sunroof frame
  3. Move to the rear of the car and check for leaks. There is no doubt where our leak is coming from…water is literally pouring out of the headliner and into the battery compartment. Note – normally most of this water would run down the D pillar and into the battery compartment…we removed the D pillar trim in this photo to better illustrate the e61 trunk leak - leak in rear of the headliner


Section 3 – Removing the D pillar trims and dropping the rear headliner.
  1. Starting on the right side of the car, remove the three small T15 torx screws anchoring the D pillar trim to the side of the vehicle.remove d pillar trim screws
  2. Next, remove the two T20 torx screws anchoring the D pillar trim to the side of the car.remove D pillar screws
  3. Grasp the top of the trim and pull straight out of the metal clip attaching it to the D e61 trunk leak - remove top part of the trim
  4. Grasp the trim at the bottom as shown and gently pull until the plastic trim clip e61 trunk leak - unsnap the bottom portion of the trim
  5. Disconnect the two electrical connectors and remove the pillar trim from the e61 trunk leak - disconnect the electrical connector from D pillar disconnect the electrical connector from D pillar remove the D pillar trim from the vehicle
  6. Repeat the above steps to remove the left D pillar trim.
  7. Next, you will need to lower the back section of the headliner so you can access the sunroof drains.
  8. Begin by removing the right and left coat hooks in the ceiling of the luggage compartment. They are held in place with T15 torx e61 trunk leak - remove coat hooks from headliner bmw e61 trunk leak - remove coat hooks from headliner
  9. Grasp the rear of the headliner and pull down to unsnap it from the ceiling of the vehicle. The headliner is held in place with two plastic clips that snap into metal clips in the roof. These plastic clips tend to break during disassembly. If yours break, you can order new ones by clicking e61 trunk leak - drop the rear of the headliner
Section 4 – Cleaning the sunroof drains

In order to repair a BMW E61 trunk leak, the sunroof drains must be thoroughly cleaned. The rubber sunroof drain lines connect to the rear of the sunroof frame and run down the D pillars and out the bottom of the vehicle.

  1. Locate the rubber sunroof drain line in the D pillar. Use a pair of scissors or utility knife to cut the rubber drain line in half. Cut it about halfway up the e61 trunk leak - cut the sunroof drain line in half bmw e61 trunk leak - cut the drain line in D pillar
  2. Follow the upper portion of the drain line above the headliner to where it attaches to the sunroof drain hole. Pull the drain line off of the drain hole. You can discard this piece of drain line…you will be replacing it with a larger diameter piece of 1/2″ clear vinyl tubing. bmw e61 trunk leak - sunroof drain diagrambmw e61 trunk leak - remove upper drain line
  3. Retract the sunroof until it is completely e61 trunk leak - retract the sunroof
  4. Attach a micro tool adapter (available at any home improvement store) to the hose of your wet-vac. Next, attach a 5’ piece ½” interior diameter clear vinyl tubing to the e61 trunk leak - attach micro adapter and 1/2" tubing to vacuum
  5. Turn on the wet-vac and slowly feed the tubing into the sunroof drain from the top of the roof. Keep pushing the tubing in until it stops at the drain hole. Verify you are at the drain hole by inserting your finger in it from the underside of the headliner…you should feel the suction (see following image). Work the tube back and forth in the sunroof drain sucking out all the dirt and e61 trunk leak - vacuum out the sunroof drainbmw e61 trunk leak - check for suction in drain hole
  6. Next, move to the rear of the car. Attach the ½” tubing to the sunroof drain hole and start the vacuum. This will suck out any debris you didn’t remove in step e61 trunk leak - vacuum out drain hole bmw e61 trunk leak - vacuum out drain hole
  7. Finally, you will need to clean the lower drain lines that direct the water out of the bottom of the vehicle. These drain lines have rubber valves on the end of them that become filled with debris. You can use a 5′ section of 4mm bicycle shifter cable (available on Amazon or any bike shop) to snake out the line and clean out the valve.
    bmw e61 trunk leak - 4mm shifter cable...use to snake the drain lines
    A 4mm Shimano bicycle shifter cable – an excellent tool for snaking out sunroof drain lines in your BMW.
  8. Using a 5’ section of bicycle shifter cable, slowly snake out the lower drain lines. DO NOT force the cable down the line. DO NOT use any type of end cap or ferrule on the cable…this can come off and get lodged in the drain line. If the cable becomes hung up, turn it 90 degrees until it continues down the drain. The goal is to get the cable down the drain and through the rubber valve under the vehicle. You will feel the cable gain resistance as it passes through the valve…work the cable back and forth to dislodge any debris caught in the e61 trunk leak - clear lower drain lines bmw e61 trunk leak - clear lower drain lines
  9. When the lower drain lines are thoroughly snaked out, attach a small section of ½” clear tubing and a small funnel to the drain line as shown in the following images. Pour a large cup of water down the drain line and verify it is quickly emptying out of the bottom of the vehicle. The water should empty out of the bottom of the car as fast as you pour it in. Repeat this process 2 or 3 times until the line is e61 trunk leak - flush lower drain lines bmw e61 trunk leak - flush lower drain linesbmw e61 trunk leak - water should flow out of bottom of car when lower drain is clear.
  10. You can see in the following image we still have a blockage in the lower drain line that won’t snake out. If the water is not draining properly and is backing up the clear vinyl tubing, remove the funnel and forcefully blow into the line. This will remove the blockage. Avoid using compressed air…this can blow the valve off of the end of the drain pipe. Once the blockage is removed, repeat step 10 and thoroughly rinse the e61 trunk leak - blockage is still in the line bmw e61 trunk leak - blow the lower line out to remove the blockage


Section 5 – Replacing, splicing and testing the drain lines

One of the issues with the rubber factory drain lines is their inside diameter. As you can see in the following image, the 1/2″ interior diameter clear vinyl tubing is significantly larger than the factory rubber hose, and can therefore remove a much higher volume of water from the sunroof e61 trunk leak - 1/2 tubing versus the original factory drain pipe

Replacing the old upper drain lines with new 1/2″ clear tubing will not only help your sunroof drain more efficiently, but it’s also a great way to monitor for future blockages (you will be able to visually see the water in the tube if it is backing up).

  1. Take a 5’ piece of ½” i.d. vinyl tubing and FIRMLY attach it to the sunroof drain holes. There is no need to heat shrink or use a hose clamp on this connection; if you push the clear tubing on as far as it will go it will not come off.
  2. Correctly route the 1/2″ tubing back to the D pillar, tucking it in behind the plastic clips along the e61 trunk leak - replace upper drain line
  3. Cut the excess off of the vinyl tubing and FIRMLY attach it to the lower drain line. You should have at least 2-3 inches of lower drain line inserted inside the vinyl tubing. Once again, there is no need to heat shrink or or use a hose clamp on this e61 trunk leak - replace upper drain line
  4. Have a helper slowly pour a cup full of water into the open sunroof drain from the top of the roof. Verify the water is easily running through the clear vinyl tubing and out the bottom of the vehicle.
  5. If everything looks good with no leaks, reassemble the vehicle following the above steps in reverse.


Section 6 – Temporary repair of headliner due to  BMW E61 Trunk Leak (optional steps)

If your sunroof drain has been overflowing for an extended period of time, you most likely will have some fabric separation at the rear of the car. The “quick fix” for this is to thoroughly brush off any loose glue and foam from the back of the fabric and the headliner, then reattach it with a proper spray fabric adhesive. Be aware that this is just a temporary fix…you will have to get your headliner professionally repaired if you want it back to its original factory condition. 
We use 3M Headliner and Fabric spray adhesive to repair our vehicles. NEVER use any type of glue or adhesive that is not specifically designed for fabric headliners…you will permanently stain the headliner and produce very poor results.

  1. We suggest wearing a pair of clean rubber gloves when reattaching your headliner to avoid getting it dirty.
  2. Place plenty of towels down to protect anything you don’t want covered with glue. The spray adhesive goes everywhere when you apply it to the fabric.
  3. Take a stiff, fine bristle hairbrush, and brush the back of the fallen fabric and the bottom of the headliner. The goal here is to remove any loose glue and foam from e61 trunk leak - temporarily fixing rear headliner bmw e61 trunk leak - temporarily fixing rear headliner
  4. Thoroughly shake the can of spray adhesive.3M headliner and fabric adhesive
  5. Apply three heavy coats of spray 3M fabric adhesive to both the fabric and the e61 trunk leak - glue fallen headliner bmw e61 trunk leak - glue fallen headliner
  6. Allow the adhesive to set up for exactly 5 minutes. Don’t wait any longer than 5 minutes…the glue sets up quickly.
  7. Firmly attach the fabric back to the headliner. Use a small foam paint roller to smooth it e61 trunk leak - fallen headliner repair
  8. If you have any wrinkles, try smoothing out with your finger tips or pulling on the e61 trunk leak - fallen headliner repair
  9. Allow to dry thoroughly for 24 hour.


BMW E61 Trunk Leak Repair Finished
If you have any questions or comments, please feel free to contact us. And congratulations for Doing It Yourself!