The car sucks cabin air in through a grill or grills in the area of the windscreen wiper hubs (well most to anyway). This area also ingests rainwater so there must be a drain or drains under there somewhere. They are usually accessible without removing anything and tend to collect leaves and get bunged up.
Havint said that if the pollen filter is dry it seems unlikely that this is the way the water is getting in. No signs or water behind the pollen filter? Is the coolant level correct? I ask because if there is a coolant leak in the cabin heater matrix or associated pipes this often ends up insode the cabin.
Take up the carpets and see if you can trace it from there?