I pulled off the sill plates and looking through the holes you could see a pool of water, I think I must have extracted a good 3-500mL of water from this area, which was fairly clear with no murkiness or gunk in it:


(credit to OMGpham for the picture)
I have never had this problem in the past, but I recently put a soft top on, and the car was outside for the last week in Sydney (which hasn't had too much rain).
Other than a clogged drain, is there any other area that it could have come from?