Hi Sara, this is one of those devilishly difficult problems to diagnose. If after you check for blocked drain holes as suggested by Steve Q, you could try the following which I posted some time ago:
"My daughter's 2012 A1 was getting rainwater in from behind the glove box. I removed the wiper arms, the plastic scuttle and saw there is a plastic channel which is supposed to drain rainwater away. This channel sits above the air intake for the a/c. The channel is quite narrow and my guess is rainwater can overflow from the sides and then find its way into the a/c blower.
I cut a 12 inch long and 1.5 inch wide strip of hard plastic and taped it under the channel so that any overflow is directed away from the a/c air intake. This was about 6 months ago and she has not had the water ingress problem since."
However, after a couple of months, we again noticed the rear passenger footwell soaked and the front passenger footwell wet. I reopened and checked the a/c air intake but that was dry. I then pulled up the carpet under the glove box and poured water across the roof on the left corner where the roof meets the windscreen. I could then see a trickle of water coming in from where the footwell meets the wheel arch.
I have now used black silicone to block the little area on the top of the windscreen on both sides of the car. I intend to remove the carpet entirely next week and have my daughter drive for a few days without it and see if the issue is finally resolved.
In your case, fingers crossed it is just the a/c drain being blocked!