Sunroofs are designed to leak water!

Sunroofs are not designed for the most part to be watertight. Sunroofs will allow water in and sunroofs are designed to handle this in their ability to get rid of the water that does get in.

Where the problems comes with sunroofs is if the drains that are designed to get rid of the water end up blocked or the water gets in via a path that was not in the original design due to a seal failure.

2 Common Reasons

1 Seal around Glass / lip is worn out, dried out, shrunk or damaged. 

Seal around sunroof glass can leak in two ways:

A - Look at the rubber seal which will probably be on the glass and see if it is still soft to touch, complete and shows no tears. As the seal ages, it will shrink causing a gap at the point of the seal where both ends connect. One test is to coat the seal in powder, then close the sunroof and run a hose over it. Anywhere where you can no longer see the powder is where the seal is leaking. If the gap is where the seal joins together, a little silicon can be used to fill the gap. 

B - As sunroof glass seal shrinks, the seal can start to leak around the glass itself allowing water to get in between the sunroof glass and rubber seal. Look for water appearing on the bottom side (inside the vehicle) of the sunroof between the seal and glass during rain. If the leak has been around long enough, you may even see rust on the metal frame that is attached to the sunroof glass. Liquid silicone applied to the top side of the seal between the sunroof glass and seal can fix this. Liquid silicone is preferred to ordinary silicone as it flows into the gaps. This second leak is more problematic as it puts rain water in locations where the drip tray installed with sunroofs does not catch the rain leading to damp car interiors.

2 Drains Blocked

Most modern power sunroofs have drains in them as there will be small leaks. Fully slide open your sunroof and look at the front of the sunroof that is part of the roof of your car. You should see at least 2 small drain holes, one on the right and the other on the left at the front. There may also be two drains at the back which you cannot see. These drain holes are connected to tubing that are usually run into the rockers or fenders of your car. Leaves, pollen and other small debris can easily block these drains. Get a gardening watering can and see if water flows through them by pouring water from the can into the drains. You also need to make sure that the drain holes in the rockers or fenders are also clear so that the rain water coming from the sunroof can escape out of the car. We had a car where the join in the seal around the sunroof glass had seperated allowing a small leak which the drains handled until a very small leaf blocked one. The end result was a soaking car which required removal of seats to dry.