In a superb display of brilliance, I managed to leave the sunroof open in my 03 Acura TL during a torrential downpour in a very humid DC in July. It took days to dry out. I threw out mats, shampooed and wetvacced the carpet. wiped off the leather seats. All is well EXCEPT when i roll down my windows. That is when I smell mold. Any suggestions on the source and how to clean it up?
Your heating and A/C system may harbor the mold you smell. You could run some spray disinfectant or mold killer through the system with the fan on high.
Why does having the windows down agravate the situation? It would seem windows up would be worse.My idea as to the source is carpet/padding still wet.
If you smell mold with the windows down and not up, then the smell must be coming from inside the doors …
Wet vacs are not enough. The padding under the carpet is still wet, and until you remove it an dry it you will have a moisture problem. You cannot get the moisture out of the padding unless you remove it from the vehicle and dry it separately. There is not a shop vac strong enough to extract this moisture from under the carpet.
I don’t understand why you smell it when your windows are down. That is exactly opposite of what I would expect.
However, I stand by my theory. Lift a corner of the carpet and stick your had under it. I bet you will feel dampness in the padding underneath. Been there, done that. It’s not easy to dry the padding, but it can be done.
I agree with the carpet padding diagnosis and as painful as it may be, sometimes it’s best to remove the carpet from the car and in some cases replace the padding.
Try removing your door inner panels and see if there’s mold there. The panels themselves may be made out of a material that provides a good growing surface.
Take a vacation to Arizona. Park the car with the windows down a sunroof open for a week. It will dry out. 
Awesome! What a great reply! The only problem with that is then I’d probably be tempted to move to Arizona permanently! Thank you!
Thanks for the input! I now have a fun weekend project
Thanks for the advice. I’ll give this a try this weekend.
Thank you for the input - I’ll keep this in mind
I can personally testify that this will work. I inherited a decade-old 1984 Buick “Olympic Edition” Le Sabre with some musty carpet developed from a chronic leak. I drove it from CNY to Tucson where it drove it for 3 years, sparingly. No more musty smell, ever, even after I moved it back to more humid, rainy climes. I almost made it to the 2000 Olympics before it became clear that the car was suffering multiple organ failure.