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

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 is 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 undrivable.

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 vehicle.

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 its 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 at 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.