Recently I discovered a lot of water in the trunk of my Seat Leon Mk3 / 5F (2014+) . After much investigation I saw drops falling in the grill on the left and right side.
As the joint between the sunroof and the car is not perfectly waterproof there is a system catching the water. The water collected there is then left out through 4 drains (2 front, 2 rear behind the back window). If those drains are blocked the water cannot leave and will go over the border and enter the car.
In my case I was lucky to have water in the trunk, so there's no damage in the inside/finishing.
The drains can be blocked at the entrance (roof) or a the exit of the tube. In my case the entrance was perfectly clean, but the exits were blocked.
This howto is to help you clean the exit from the front of the car, and the rear of the car.