i had the leaking
problem in my leon when purchased,
the fixes where to remove all old foam seal from the doors and install butyl. this is the sea lthats on the inner door carrier once you unbolt it you can peal off the old seal and install the new butyl tape (Brilliant stuff)
put vaseline on door seals to improve water tightness.
take out foam seal in pollen filter tray and install butyl.
makesure the rear window washer jet pipe that runs in with the wiring loom behind the heater fan isnt
broken\fractured or disconnected, (mine was disconnected, but my leak was coming in through the
inner carrier seals and pollen filter. which is now fixed.
take out glove box and undo the 2 screws under the fan to drop the fan out and reveal if any water is in there to find out if this is the cause of your
problem.