Clearing the sunroof drains to avoid a wet interior or fixing a broken line
difficulty: 1/5
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Introduction

There are water drains at the corners of the sunroof that let water drain out to an exit at the door hinge.  If it gets blocked by whatever, the water will back up and empty into your interior, causing possible water damage to electronics, mold, etc..  Regular cleaning will help prevent this condition.  Parking the car with the sunroof open will cause faster drain clogging.  The mk3 passat had the sunroof drain exit into the fender.  All other cars have the sunroof drain exit as pictured below.  Pics from volksbloggin.

Warning - if you do poke a hole into the line or it's already broken, instead of taking apart the interior, just feed a new line into the old line as pictured below.

Parts

weedwacker line or something stiff and flexible but not hard or sharp like a coat hanger (too hard)
some water to flush out the drain

Cleaning Procedure

Open the sunroof and front doors.  Locate the drains at the top and the drains in the door hinge.  In the mk3 passat the drain outputs are in the fender well, all other VW TDI, the drains are in the door hinge. 

Pour a little water into the sunroof drain at the top and check for proper flow.  This will also help clean out any small particles.  I don't recommend compressed air because it might blow loose the line.  If this happens, you have to remove the interior panels to repair the line.  If it's okay, pour a lot of water in there to flush any particles out.  If the line gets dislodged or you find water leaking into the interior, repair it using the steps below.

If it's not flowing well, use a weedwacker line to poke it clean little by little, or try twisting the rubber exit drain with your fingers.  Do not use a coat hanger or anything that could puncture the drain line or else you will have to remove the interior panels to repair it, so don't force the weedwacker line!  

Follow up with water at the sunroof drain to clear out any particles.  It should easily drain out as seen below.

Repairing a broken line

If you find that there is a leak and water is entering the cabin, you must repair it to prevent electrical and interior damage.  The normal procedure is to take the interior panel "A" pillar, the one by the windshield apart and replace the line.  There may be an airbag in there, so disconnect the battery and follow all applicable cautions in your factory service manual if you have curtain airbags.  

An alternative is to put a new line inside the old line.  Snake a new line though the old line and trim to fit.  If it doesn't want to go in through the top, snake the line in through the bottom.

You can put a fitting around the end of the hose to prevent it from falling in any further.  Use silicone sealant to hold the upper end in place and let dry.

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