Why sunroofs leak

Contrary to popular belief, sunroofs are not watertight.  A controlled amount of water gets past the rubber seal and drops into the sunroof gutter.  There is a drain tube on each corner of the sunroof gutter.  The problem is that not only water drops onto the gutter, but dirt and small debris also drop in the gutter.  The dirt and debris wash into the drain tubes and can eventually partially clog, or fully clog the tubes.  Once the tube(s) get clogged they can no longer properly drain the water and a leak is created.

The leak can either be from the headliner tray or in the footwell of either one or both sides of the car depending on which tube is obstructed.